Methods and compositions for the treatment of psychotic disorders through the identification of the SULT4A1-1 haplotype

ABSTRACT

Methods and compositions that relate to genetic markers of psychotic disorders, e.g., schizophrenia (SZ), are provided. For example, in certain aspects methods for determinations of a SULT4A1-1 haplotype are described. Furthermore, the invention provides methods and compositions involving treatment of psychotic disorders using the haplotype status.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation-in-part of U.S. application Ser. No.12/859,056, filed Aug. 18, 2010, and U.S. application Ser. No.12/858,971, filed Aug. 18, 2010, each of which is a continuation-in-partof U.S. application Ser. No. 12/646,723, filed Dec. 23, 2009, now issuedas U.S. Pat. No. 7,790,396, and U.S. application Ser. No. 12/612,438,filed Nov. 4, 2009. The entire contents of each of the referencedapplications are incorporated herein by reference.

This invention was made with government support under SBIR grantMH078347 and grants N01 MH900001 and MH074027 awarded by NationalInstitutes of Mental Health. The government has certain rights in theinvention.

BACKGROUND OF THE INVENTION

1. Field of the Invention

The present invention relates generally to the field of psychoticdisorders, such as schizophrenia and bipolar disorders. Moreparticularly, it concerns genetic markers of antipsychotic response, forexample, genes and genetic markers that influence or predict a person'slikely response to antipsychotic medications.

2. Description of Related Art

Numerous drugs exist to treat psychotic disorders, such as schizophrenia(SZ), related SZ-spectrum disorders (including schizotypal personalitydisorder (SPD) and schizoaffective disorder (SD)), and bipolar disorders(BD). Most of these drugs fall into one of two categories, typical(first generation) and atypical (second generation).

Although head to head studies of large groups of patients, either in theacute phase or outpatient treatment, show that most atypicalantipsychotic drugs are equally efficacious for positive symptoms, thereare individual differences in response to specific drugs based ondifferences in drug pharmacology and metabolism, combined with geneticdifferences between patients. There are currently no proven ways toidentify which antipsychotic drug is optimal for a given patient. Thus,patients switch from one drug to another when response is not consideredto be adequate or side effects are intolerable. This switching ofmedication incurs a variety of increased costs, both economic andpatient and caregiver hardship. On average, each patient may changemedications three times before finding one that works. Additionally, thecurrent drugs have significant side-effects. This combination ofside-effects and limited efficacy create a vast unmet need for selectingthe optimal antipsychotic for each patient.

Moreover, the limited or partial response that is often seen withantipsychotics leads to polypharmacy, where physicians prescribe two ormore antipsychotic drugs plus mood stabilizers and/or antidepressants.Polypharmacy increases medication costs and significantly increases thelikelihood of adverse advents and drug interactions (Stahl and Grady,2006).

Pharmacogenomics, using genetic variation to predict altered responseand side-effects profiles, will be important for enhanced patient caregoing forward. There continues to exist, therefore, a need to identifyspecific genetic variations that are associated with treatment outcomesfor psychotic disorders.

SUMMARY OF THE INVENTION

The invention is in part based on the finding that a particularhaplotype, which the inventors refer to as the SULT4A1-1 haplotype, is abiomarker that can be used for selecting a more appropriateantipsychotic treatment plan for a particular subject. For example, theinventors have discovered that patients that have a SULT4A1-1 haplotyperespond better when treated with olanzapine than SULT4A1-1 positivepatients treated with risperidone, and respond better than SULT4A1-1negative patients treated with olanzapine. Similarly, the inventors havediscovered that patients that have a SULT4A1-1 haplotype respond betterwhen treated with quetiapine than SULT4A1-1 negative patients treatedwith quetiapine. Further, the inventors have discovered that patientsthat do not have a SULT4A1-1 haplotype respond better when treated withrisperidone than SULT4A1-1 positive patients treated with risperidone.Thus, prior determination of a patient's SULT4A1-1 haplotype status canaid in the development of an optimal antipsychotic treatment regimen.

Thus, an aspect of the invention involves determining whether geneticmaterial of the subject comprises a SULT4A1-1 haplotype. Of course, tomeet the need to transfer and store genetic information, the results ofthe determination will preferably be recorded and maintained in atangible medium, such as a computer-readable disk, a solid state memorydevice, an optical storage device or the like, more specifically, astorage device such as a hard drive, a Compact Disk (CD) drive, a floppydisk drive, a tape drive, a random access memory (RAM), etc.

One preferred manner of obtaining the genetic haplotype informationinvolves analyzing the genetic material of the subject to determine thepresence or absence of the SULT4A1-1 haplotype. This can beaccomplished, for example, by testing the subject's genetic materialthrough the use of a biological sample. In certain embodiments, themethods set forth will thus involve obtaining a biological sample fromthe subject and testing the biological sample to identify whether aSULT4A1-1 haplotype is present. The biological sample may be anybiological material that contains DNA or RNA of the subject, such as anucleated cell source. Non-limiting examples of cell sources availablein clinical practice include hair, skin, nucleated blood cells, buccalcells, any cells present in tissue obtained by biopsy or any other cellcollection method. The biological sample may also be obtained from bodyfluids, including without limitation blood, saliva, sweat, urine,amniotic fluid (the fluid that surrounds a fetus during pregnancy),cerebrospinal fluid, feces, and tissue exudates. DNA may be extractedfrom the biologic sample such as the cell source or body fluid using anyof the numerous methods that are standard in the art.

Determining whether the genetic material exhibits a SULT4A1-1 haplotypepolymorphism can be by any method known to those of ordinary skill inthe art, such as genotyping (e.g., SNP genotyping) or sequencing.Techniques that may be involved in this determination are well-known tothose of ordinary skill in the art. Examples of such techniques includeallele specific oligonucleotide hybridization, size analysis,sequencing, hybridization, 5′ nuclease digestion, single-strandedconformation polymorphism analysis, allele specific hybridization,primer specific extension, and oligonucleotide ligation assays.Additional information regarding these techniques is discussed in thespecification below.

For haplotype determinations, the sequence of the extracted nucleic acidof the subject may be determined by any means known in the art,including but not limited to direct sequencing, hybridization withallele-specific oligonucleotides, allele-specific PCR, ligase-PCR, HOTcleavage, denaturing gradient gel electrophoresis (DDGE), andsingle-stranded conformational polymorphism (SSCP) analysis. Directsequencing may be accomplished by any method, including withoutlimitation chemical sequencing, using the Maxam-Gilbert method, byenzymatic sequencing, using the Sanger method, mass spectrometrysequencing, and sequencing using a chip-based technology. In particularembodiments, DNA from a subject is first subjected to amplification bypolymerase chain reaction (PCR) using specific amplification primers. Insome embodiments, the method further involves amplification of a nucleicacid from the biological sample. The amplification may or may notinvolve PCR. In some embodiments, the primers are located on a chip.

In specific embodiments, the subject is a human. For example, in someembodiments the human is a subject who has, is suspected to have, or isat risk of a psychotic disorder, such as schizophrenia, schizotypalpersonality disorder (SPD), schizoaffective disorder (SD), or bipolardisorder (BD). In one embodiment, the subject is a patient havingpreviously diagnosed a psychotic disorder (e.g., a patient sufferingfrom early, intermediate or aggressive psychotic disorder). In someembodiments, the subject is of Caucasian (CA) descent, i.e., has one ormore ancestors who are CA.

Moreover, the inventors contemplate that the genetic structure andsequence, including SNP profiles, of individual subjects will at somepoint be widely or generally available, or will have been developed byan unrelated third party. In such instances, there will be no need totest or analyze the subject's biological material again. Instead, thegenetic information will in such cases be obtained simply by analyzingthe sequencing or genotyping outcome of the subject, for example, a SNPprofile, a whole or partial genome sequence, etc. These outcome can thenbe obtained from or reported by a sequencing or a genotyping service, alaboratory, a scientist, or any genetic test platforms.

In some further aspects, the method may further comprise reporting thedetermination to the subject, a health care payer, an attendingclinician, a pharmacist, a pharmacy benefits manager, or any person thatthe determination may be of interest.

In certain embodiments, there is also provided a method of developing apharmacotherapeutic treatment plan for a subject having or suspected ofhaving a psychotic disorder comprising determining the SULT4A1-1haplotype status of the patient, wherein a) if the subject comprises aSULT4A1-1 haplotype, the subject is more likely to exhibit a favorableresponse to olanzapine; and b) if the subject does not comprise aSULT4A1-1 haplotype, the subject is less likely to exhibit a favorableresponse to olanzapine; and developing the pharmacotherapeutic treatmentplan. For example, if the subject comprises a SULT4A1-1 haplotype, thenthe method may further comprise treating the subject with olanzapine. Ifthe subject does not comprise the SULT4A1-1 haplotype, then the methodmay further comprise treating the subject with an anti-psychotictreatment other than olanzapine, such as treating with risperidone, orperphenazine.

In certain embodiments, there is also provided a method of determiningelevated risk of a patient to discontinue treatment with olanzapine dueto a treatment-emergent adverse event, comprising determining theSULT4A1-1 haplotype in a patient sample, wherein a) if the human subjectcomprises the SULT4A1-1 haplotype, the subject is more likely to exhibita propensity to continue treatment; and b) if the subject does notcomprise the SUTL4A1-1 haplotype, the subject is more likely to exhibita propensity to discontinue treatment due to a treatment-emergentadverse event.

In certain embodiments, there is also provided a method of selecting apharmacotherapeutic treatment plan for a human subject having thepotential to experience a treatment-emergent adverse event when treatedwith olanzapine, comprising determining the SULT4A1-1 haplotype in asample, wherein a) if the human subject does not comprise the SULT4A1-1haplotype the subject is more likely to experience a treatment-emergentadverse event when treated with olanzapine; and b) if the subjectcomprises the SUTL4A1-1 haplotype the subject is not more likely toexperience a treatment-emergent adverse event when treated witholanzapine; selecting a pharmacotherapeutic treatment plan based on theSULT4A1-1 haplotype; and treating the subject with the selectedpharmacotherapeutic treatment.

Certain aspects of the invention may involve a method for treating asubject having a psychotic disorder and determined to have a SULT4A1-1haplotype, comprising treating the subject with olanzapine. In somefurther aspects, the invention may include a method for treating asubject having a psychotic disorder and determined not to have aSULT4A1-1 haplotype, comprising treating the subject with anon-olanzapine anti-psychotic treatment, such as treating withrisperidone, ziprasidone, or perphenazine. In certain embodiments, thepsychotic disorder is schizophrenia.

In other embodiments, there is provided a method for determiningresponse to treatment with risperidone for a human subject having orsuspected of having schizophrenia comprising determining the SULT4A1-1haplotype in a sample, wherein a) if the human subject comprises theSULT4A1-1 haplotype, the subject is less likely to exhibit a favorableresponse to risperidone; and b) if the subject does not comprise theSUTL4A1-1 haplotype, the subject is more likely to exhibit a favorableresponse to risperidone.

In other embodiments, there is provided a method for determiningelevated risk of a patient to discontinue treatment with risperidone dueto a treatment-emergent adverse event or lack of efficacy comprisingdetermining the SULT4A1-1 haplotype in a sample, wherein a) if the humansubject comprises the SULT4A1-1 haplotype, the subject is more likely toexhibit a propensity to discontinue treatment due to atreatment-emergent adverse event or lack of efficacy; and b) if thesubject does not comprise the SUTL4A1-1 haplotype, the subject is morelikely to exhibit a propensity to continue treatment.

In certain embodiments, there is also provided a method for selecting apharmacotherapeutic treatment plan for a human subject having thepotential for suffering a treatment-emergent adverse event or lack ofefficacy when treated with risperidone, comprising determining theSULT4A1-1 haplotype in a sample, wherein a) if the human subjectcomprises the SULT4A1-1 haplotype, the subject is more likely toexperience a treatment-emergent adverse event or lack of efficacy whentreated with risperidone; and b) if the subject does not comprise theSUTL4A1-1 haplotype, the subject is not more likely to experience atreatment-emergent adverse event or lack of efficacy when treated withrisperidone; selecting a pharmacotherapeutic treatment plan based on theSULT4A1-1 haplotype; and treating the subject with the selectedpharmacotherapeutic treatment.

Certain aspects of the invention may involve a method for treating asubject having a psychotic disorder and determined to not have theSULT4A1-1 haplotype, comprising treating the subject with risperidone.In some further aspects, the invention may include a method for treatinga subject having a psychotic disorder and determined to have a SULT4A1-1haplotype, comprising treating the subject with a non-risperidoneanti-psychotic treatment such as treating with olanzapine, quetiapine,ziprasidone, or perphenazine. In certain embodiments, the psychoticdisorder is schizophrenia.

In other embodiments, there is provided a method for determiningresponse to treatment with quetiapine for a human subject having orsuspected of having schizophrenia comprising determining the SULT4A1-1haplotype in a sample, wherein if the human subject comprises theSULT4A1-1 haplotype the subject is more likely to exhibit a favorableresponse to quetiapine and if the subject does not comprise theSULT4A1-1 haplotype the subject is less likely to exhibit a favorableresponse to quetiapine.

In certain embodiments, there is also provided a method for treating ahuman subject having or suspected of having a psychotic disordercomprising a) selecting a subject that has been determined to have aSULT4A1-1 haplotype, defined as a haplotype comprising a C allele atrs763120, a combination of an A allele at rs2285162 and a G allele atrs2285167, or the combination of a T allele atrs2285166 and G allele atrs2285167, and treating the subject with quetiapine or olanzapine; or b)selecting a subject that has been determined not to have the SULT4A1-1haplotype and treating the subject with an anti-psychotic treatmentother than quetiapine or olanzapine.

Certain aspects of the invention may involve a method for treating asubject having a psychotic disorder and determined to have a SULT4A1-1haplotype, comprising treating the subject with quetiapine orolanzapine. In some further aspects, the invention may include a methodfor treating a subject having a psychotic disorder and determined not tohave a SULT4A1-1 haplotype, comprising treating the subject with a ananti-psychotic treatment other than quetiapine or olanzapine, such astreating with risperidone, ziprasidone, or perphenazine. In certainembodiments, the psychotic disorder is schizophrenia.

Certain aspects of the invention may involve a method for treating asubject comprising selecting a subject that is determined to have aSULT4A1-1 haplotype and developing an appropriate treatment plan. Otheraspects of the invention may involve a method for treating a subjectcomprising selecting a subject that is determined not to have aSULT4A1-1 haplotype and developing an appropriate treatment plan. Priordetermination of a patient's SULT4A1-1 haplotype status may be obtainedfrom or reported by a sequencing or a genotyping service, a laboratory,a scientist, or any genetic test platforms.

The SULT4A1-1 haplotype characterization may also apply to diagnosis andprognosis of psychotic disorders. For example, there may be provided amethod of assessing the severity of such a disorder, comprisingobtaining genetic information about the subject by the methods disclosedabove, wherein if the subject comprises a SULT4A1-1 haplotype, thesubject is at a higher risk for having a more severe disorder, andwherein if the subject does not comprise the SULT4A1-1 haplotype, thesubject is at a lower risk for having a more severe disorder. Theassessment may be stored in a tangible medium, such as acomputer-readable disk, a solid state memory device, and an opticalstorage device.

Certain aspects of the present invention also contemplate thepreparation of kits or arrays for use in accordance with the presentinvention. Suitable kits include various reagents for use in accordancewith the present invention in suitable containers and packagingmaterials, including tubes, vials, and shrink-wrapped and blow-moldedpackages. Such an array or a kit may comprise a plurality of primers orprobes specific for a SULT4A1-1 haplotype. The array may be a genotypingchip. Also a tangible, computer-readable medium comprising a SNP profileof a subject may also be provided, wherein the SNP profile exhibits thepresence or absence of a SULT4A1-1 haplotype.

Embodiments discussed in the context of methods and/or compositions ofthe invention may be employed with respect to any other method orcomposition described herein. Thus, an embodiment pertaining to onemethod or composition may be applied to other methods and compositionsof the invention as well.

As used herein the specification, “a” or “an” may mean one or more. Asused herein in the claim(s), when used in conjunction with the word“comprising”, the words “a” or “an” may mean one or more than one.

The use of the term “or” in the claims is used to mean “and/or” unlessexplicitly indicated to refer to alternatives only or the alternativesare mutually exclusive, although the disclosure supports a definitionthat refers to only alternatives and “and/or.” As used herein “another”may mean at least a second or more.

Throughout this application, the term “about” is used to indicate that avalue includes the inherent variation of error for the device, themethod being employed to determine the value, or the variation thatexists among the study subjects.

Other objects, features and advantages of the present invention willbecome apparent from the following detailed description. It should beunderstood, however, that the detailed description and the specificexamples, while indicating preferred embodiments of the invention, aregiven by way of illustration only, since various changes andmodifications within the spirit and scope of the invention will becomeapparent to those skilled in the art from this detailed description.

BRIEF DESCRIPTION OF THE DRAWINGS

The following drawings form part of the present specification and areincluded to further demonstrate certain aspects of the presentinvention. The invention may be better understood by reference to one ormore of these drawings in combination with the detailed description ofspecific embodiments presented herein.

FIG. 1: Linkage disequilibrium for the Caucasian sample. The Haploviewoutput shows pairwise correlation coefficients (r² values in % are givenin the diamonds) for the 11 SULT4A1 SNPs from the CATIE study (N=836persons). Based on the total sample of cases and controls, Haploviewidentifies a single haplotype block for the 11 SNPs (Barrett et al.,2005). The locations of previously studied SNPs, rs138097 (the SNP is inposition 31 of SEQ ID NO:8) and rs138110 (the SNP is in position 31 ofSEQ ID NO:13), are indicated by arrows. Only the latter was included inthe CATIE study. Previously studied marker rs138060 (the SNP is inposition 31 of SEQ ID NO:1) is located approximately 5 kb to the left ofrs138067 (the SNP is in position 31 of SEQ ID NO:2), outside the regioncovered by the SULT4A1 SNPs in CATIE.

FIG. 2: Linkage disequilibrium for the African American sample. TheHaploview output shows pairwise correlation coefficients (r² values in%) for the 11 CATIE SNPs (N=442 persons).

FIG. 3: Response of SULT4A1-1 positive subjects in CATIE at variousresponse thresholds.

FIG. 4: Response of SULT4A1-1 negative subjects in CATIE at variousresponses thresholds.

FIG. 5: Percentage of SULT4A1-1 positive patients remaining in phase 1of the CATIE trial at various time points.

FIG. 6: Percentage of SULT4A1-1 negative patients remaining in phase 1of the CATIE trial at various time points.

FIG. 7: An exemplary embodiment of risk management involving SULT4A1-1determination.

FIG. 8: Kaplan-Meier survival curves for the SULT4A1-1 negative andSULT4A1-1 positive patient populations. Each plot corresponds to anindividual atypical antipsychotic in the CATIE trial. The curves modelthe fraction of the trial population that will not have ahospitalization event as a function of time. Survival fractions areadjusted for the number of subjects remaining in the trial at each timepoint. Vertical slashes correspond to patients discontinuing the drug,either due to drug switching or stopping participation in the trial.

DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS

Choosing the correct antipsychotic medication for patients sufferingfrom severe neuropsychiatric illnesses is a major challenge. Fewer thanone in three patients suffering from schizophrenia and related disorderswill have a robust improvement in symptoms on the first antipsychoticdrug prescribed. One out of three patients will be resistant to commonlyused drugs. Furthermore, the metabolic side-effects of antipsychoticdrugs, most commonly seen with olanzapine and clozapine, result in lowcompliance, with 50% of patients discontinuing drug use within 6 monthsof prescription, leading to relapse (return of psychosis) andhospitalization.

Therefore, methods and compositions of the present invention will helpto meet this challenge by assisting physicians, patients, lab, orpharmacists with selection or recommendation of appropriateantipsychotic medication. Specifically, the present inventors have useda specific haplotype of the SULT4A1 gene for pharmacogenomicapplications in related psychotic disorders, i.e., assessing the impactof genetic variation on drug response and side-effect profiles.

Examples of variation in drug response include any of the following:efficacy, side-effect profile, treatment maintenance and discontinuationrates, return to work status, hospitalizations, suicidality, totalhealthcare cost, social functioning scales, response tonon-pharmacological treatments, and dose response curves. Efficacyincludes but is not limited to the following definition: >=20 decreasein Total PANSS score. Side-effect profile includes one or more of weightgain, metabolic dysfunction, lipid dysfunction, movement disorders, andextrapyramidal symptoms.

Further embodiments and advantages of the invention are described below.

I. Definitions

As defined herein, “Schizophrenia” or “SZ” includes the SZ-spectrumdisorders, Schizotypal Personality Disorder (SPD) and SchizoaffectiveDisorder (SD), as well as Schizophrenia under the narrower, DSM-IVdefinition.

As used herein, a “haplotype” is one or a set of markers (e.g.,polymorphisms) that are grouped closely together on a given chromosomeand are usually inherited as a group. As used herein, the term“polymorphism” refers to the condition in which there is a variation inthe DNA sequence between some members of a species. A haplotype caninclude, but not be limited to, a variety of genetic markers, includingindels (insertions or deletions of the DNA at particular locations onthe chromosome); single nucleotide polymorphisms (SNPs) in which aparticular nucleotide is changed; microsatellites; and minisatellites.

As used herein, a “SULT4A1-1 haplotype,” i.e., a “SULT4A1-1 positivehaplotype,” refers to a haplotype comprising rs763120(C) (a C allele inposition 31 of SEQ ID NO:15), a combination of rs2285162(an A allele atposition 31 of SEQ ID NO:6)-rs2285167(a G allele at position 31 of SEQID NO:9), a combination of rs2285166(a T allele at position 31 of SEQ IDNO:14)-rs2285167(G), or a haplotype that is in complete linkagedisequilibrium with the combination rs2285162(A)-rs2285167(G) orrs2285166(T)-rs2285167(G), such as a haplotype comprising rs763120 (a Callele at position 31 of SEQ ID NO:15). The sequence identifiers areintended for SNP sequence identification only and an ordinary person ofskill in the art would recognize some subjects may have sequenceheterogeneity or polymorphism at other positions of those sequences.

“Linkage disequilibrium” occurs when the observed frequencies ofassociations of alleles for different polymorphisms in a population donot agree with frequencies predicted by multiplying together the allelefrequencies for the individual genetic markers, thus resulting in aspecific haplotype in the population.

The term “chromosome” as used herein refers to a gene carrier of a cellthat is derived from chromatin and comprises DNA and protein components(e.g., histones). The conventional internationally recognized individualhuman genome chromosome numbering identification system is employedherein. The size of an individual chromosome can vary from one type toanother with a given multi-chromosomal genome and from one genome toanother. In the case of the human genome, the entire DNA mass of a givenchromosome is usually greater than about 100,000,000 base pairs. Forexample, the size of the entire human genome is about 3×10⁹ base pairs.

The term “gene” refers to a DNA sequence in a chromosome that codes fora product (either RNA or its translation product, a polypeptide). A genecontains a coding region and includes regions preceding and followingthe coding region (termed respectively “leader” and “trailer”). Thecoding region is comprised of a plurality of coding segments (“exons”)and intervening sequences (“introns”) between individual codingsegments.

The term “probe” refers to an oligonucleotide. A probe can be singlestranded at the time of hybridization to a target. As used herein,probes include primers, i.e., oligonucleotides that can be used to primea reaction, e.g., a PCR reaction.

The term “label” or “label containing moiety” refers in a moiety capableof detection, such as a radioactive isotope or group containing same,and nonisotopic labels, such as enzymes, biotin, avidin, streptavidin,digoxygenin, luminescent agents, dyes, haptens, and the like.Luminescent agents, depending upon the source of exciting energy, can beclassified as radioluminescent, chemiluminescent, bioluminescent, andphotoluminescent (including fluorescent and phosphorescent). A probedescribed herein can be bound, e.g., chemically bound tolabel-containing moieties or can be suitable to be so bound. The probecan be directly or indirectly labeled.

The term “direct label probe” (or “directly labeled probe”) refers to anucleic acid probe whose label after hybrid formation with a target isdetectable without further reactive processing of hybrid. The term“indirect label probe” (or “indirectly labeled probe”) refers to anucleic acid probe whose label after hybrid formation with a target isfurther reacted in subsequent processing with one or more reagents toassociate therewith one or more moieties that finally result in adetectable entity.

The terms “target,” “DNA target,” or “DNA target region” refers to anucleotide sequence that occurs at a specific chromosomal location. Eachsuch sequence or portion is preferably at least partially, singlestranded (e.g., denatured) at the time of hybridization. When the targetnucleotide sequences are located only in a single region or fraction ofa given chromosome, the term “target region” is sometimes used. Targetsfor hybridization can be derived from specimens which include, but arenot limited to, chromosomes or regions of chromosomes in normal,diseased or malignant human cells, either interphase or at any state ofmeiosis or mitosis, and either extracted or derived from living orpostmortem tissues, organs or fluids; germinal cells including sperm andegg cells, or cells from zygotes, fetuses, or embryos, or chorionic oramniotic cells, or cells from any other germinating body; cells grown invitro, from either long-term or short-term culture, and either normal,immortalized or transformed; inter- or intraspecific hybrids ofdifferent types of cells or differentiation states of these cells;individual chromosomes or portions of chromosomes, or translocated,deleted or other damaged chromosomes, isolated by any of a number ofmeans known to those with skill in the art, including libraries of suchchromosomes cloned and propagated in prokaryotic or other cloningvectors, or amplified in vitro by means well known to those with skill;or any forensic material, including but not limited to blood, or othersamples.

The term “hybrid” refers to the product of a hybridization procedurebetween a probe and a target. The term “hybridizing conditions” hasgeneral reference to the combinations of conditions that are employablein a given hybridization procedure to produce hybrids, such conditionstypically involving controlled temperature, liquid phase, and contactbetween a probe (or probe composition) and a target. Conveniently andpreferably, at least one denaturation step precedes a step wherein aprobe or probe composition is contacted with a target. Guidance forperforming hybridization reactions can be found in Ausubel et al.(2003). Aqueous and nonaqueous methods are described in that referenceand either can be used. Hybridization conditions may be a 50% formamide,2×SSC wash for 10 minutes at 45° C. followed by a 2×SSC wash for 10minutes at 37° C.

Calculations of “identity” between two sequences can be performed asfollows. The sequences are aligned for optimal comparison purposes(e.g., gaps can be introduced in one or both of a first and a secondnucleic acid sequence for optimal alignment and non-identical sequencescan be disregarded for comparison purposes). The length of a sequencealigned for comparison purposes is at least 30%, e.g., at least 40%,50%, 60%, 70%, 80%, 90% or 100%, of the length of the referencesequence. The nucleotides at corresponding nucleotide positions are thencompared. When a position in the first sequence is occupied by the samenucleotide as the corresponding position in the second sequence, thenthe molecules are identical at that position. The percent identitybetween the two sequences is a function of the number of identicalpositions shared by the sequences, taking into account the number ofgaps, and the length of each gap, which need to be introduced foroptimal alignment of the two sequences.

The comparison of sequences and determination of percent identitybetween two sequences can be accomplished using a mathematicalalgorithm. In some embodiments, the percent identity between twonucleotide sequences is determined using the GAP program in the GCGsoftware package, using a Blossum 62 scoring matrix with a gap penaltyof 12, a gap extend penalty of 4, and a frameshift gap penalty of 5.

As used herein, the term “substantially identical” is used to refer to afirst nucleotide sequence that contains a sufficient number of identicalnucleotides to a second nucleotide sequence such that the first andsecond nucleotide sequences have similar activities. Nucleotidesequences that are substantially identical are at least 80%, e.g., 85%,90%, 95%, 97% or more, identical.

The term “nonspecific binding DNA” refers to DNA which is complementaryto DNA segments of a probe, which DNA occurs in at least one otherposition in a genome, outside of a selected chromosomal target regionwithin that genome. An example of nonspecific binding DNA comprises aclass of DNA repeated segments whose members commonly occur in more thanone chromosome or chromosome region. Such common repetitive segmentstend to hybridize to a greater extent than other DNA segments that arepresent in probe composition.

As used herein, the term “stratification” refers to the creation of adistinction between subjects on the basis of a characteristic orcharacteristics of the subjects. Generally, in the context of clinicaltrials, the distinction is used to distinguish responses or effects indifferent sets of patients distinguished according to the stratificationparameters. In some embodiments, stratification includes distinction ofsubject groups based on the presence or absence of a SULT4A1-1 haplotypedescribed herein. The stratification can be performed, e.g., in thecourse of analysis, or can be used in creation of distinct groups or inother ways.

As used herein, “Typical” antipsychotics refer to so called firstgeneration or classical antipsychotics. This class of drugs was firstdeveloped in the 1950s. Some examples include: Chlorpromazine(Largactil, Thorazine), Fluphenazine (Prolixin), Haloperidol (Haldol,Serenace), Molindone, Thiothixene (Navane), Thioridazine (Mellaril),Trifluoperazine (Stelazine), Loxapine (Loxapac, Loxitane), Perphenazine,Prochlorperazine (Compazine, Buccastem, Stemetil), Pimozide (Orap),Zuclopenthixol (Clopixol). This class of drug can cause serious adverseevents, particularly Tardive Dyskinesia, a movement disorder.

As used herein, “Atypical” antipsychotics refer to a newer class ofantipsychotic drugs first introduced in the 1990s. This class of drugsincludes the following examples:

Clozapine (Clozaril) (FDA-approval: 1990): Available in oral tablets anddissolving tablets (FazaClo).

Risperidone (Risperdal) (FDA-approval: 1993): Available in oral tablets,dissolving tablets, liquid form, and extended release intramusclarinjection.

Olanzapine (Zyprexa) (FDA-approval: 1996): Available in oral tablets,dissolving tablets, and intramuscular injection.

Quetiapine (Seroquel) (FDA-approval: 1997): Available only in oraltablets.

Ziprasidone (Geodon) (FDA-approval: 2001): Available in oral capsulesand intramuscular injection.

Aripiprazole (Abilify) (FDA-approval: 2002): Available in oral tabletsand dissolving tablets.

Paliperidone (Invega) (FDA-approval: 2006): Available inextended-release oral tablets.

Asenapine (Saphris) (FDA-approval: 2009): Available in sublingualtablets.

Lurasidone (Latuda) (FDA-approval: 2010): Available in oral tablets.

Iloperidone (Fanapta or Zomaril): FDA has accepted NDA as of Nov. 27,2007.

Sertindole (Serlect) (Not approved by the FDA for use in the USA).

Zotepine (Not approved by the FDA for use in the USA).

Amisulpride (Not approved by the FDA for use in the USA).

Bifeprunox (Not approved by the FDA for use in the USA).

Melperone: Approved in Europe. Currently in clinical trials in the USA.

Atypicals have a superior side-effect profile for the serious adverseevent Tardive Dyskinesia. However, the atypicals can cause metabolicdisturbances leading to weight gain and metabolic syndrome.

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. Methods and materials aredescribed herein for use in the present invention; other, suitablemethods and materials known in the art can also be used. The materials,methods, and examples are illustrative only and not intended to belimiting. All publications, patent applications, patents, sequences,database entries, and other references mentioned herein are incorporatedby reference in their entirety. In case of conflict, the presentspecification, including definitions, will control.

II. SULT4A1-1 Haplotype

In certain aspects, the present invention involves determination of aSULT4A1-1 haplotype and use of the specific haplotype to optimizetreatments for psychotic disorders. For example, the invention mayenhance drug safety and improve treatment outcome.

The sulfotransferase-4A1 (SULT4A1) gene encodes the major cytoplasmicsulfotransferase in the central nervous system and is believed to beinvolved in neurotransmitter metabolism and function (Iali-Hassani etal., 2007; Liyou et al., 2003; Minchin et al., 2008). Certain alleles ofthe gene are over-transmitted to offspring with schizophrenia infamilies having multiple affected individuals (Brennan and Condra,2005), and genotypes for SNPs in this gene are associated withpsychopathology and cognition in patients suffering from schizophreniaand schizoaffective disorder (Meltzer et al., 2008).

The inventors used samples from the Clinical Antipsychotic Trials ofIntervention Effectiveness (CATIE), a large federally funded clinicaltrial designed to assess the efficacy of antipsychotics in a real worldsetting (Lieberman et al., 2005; Stroup et al., 2003), to identifycommon variants of the SULT4A1 gene relating to elevated levels ofbaseline psychopathology and to explore gene-based differentialresponses of patients suffering from schizophrenia and related disorders(schizoaffective disorder and bipolar disorder) to atypicalantipsychotic drugs.

A commonly occurring variation in the SULT4A1 gene correlated withatypical antipsychotic response was characterized. Specifically, theSULT4A1-1 haplotype can be tagged by two single nucleotide polymorphisms(SNPs): the rs2285167 (G) allele in combination with either thers2285162(A) allele or the rs2285166(T). Since the latter two SNPs arein complete linkage disequilibrium, they can be used interchangeably.Alternatively, the SULT4A1-1 haplotype can be tagged by any SNPs or SNPcombinations which are exchangeable with these two-SNP combinations,such as a single SNP rs763120 (C).

The SULT4A1-1 haplotype was also selected as the biomarker of interestbased on results showing associations between this haplotype and diseaseseverity. The SULT4A1-1 haplotype occurs at a frequency of approximately11.7% in Caucasians and is found at expected levels based onHardy-Weinberg predictions, such that approximately 23% of patientscarry it.

III. Haplotype Determination

The invention includes methods for determination of SULT4A1 haplotypesin order to select optimal treatments. One or more markers, such as SNPswithin SULT4A1 gene (exemplary SNPs like rs2285162(A), rs2285166(T),rs2285167(G), and rs763120 (C)), can be used to determine a SULT4A1-1haplotype as defined above. Using the exemplary SNP markers or SNPs incomplete linkage disequilibrium with the exemplary SNPs, one candetermine the haplotype. Using these haplotypes, one can assign subjectsto specific categories based on the evaluation of haplotypes present inthe subject and select optimal treatments (atypical antipsychotic,typical antipsychotic, and/or psychosocial intervention) for patients.

Determining a haplotype can, but need not, include obtaining a samplecomprising DNA from a subject, and/or assessing the identity, presenceor absence of one or more genetic markers for the SULT4A1-1 haplotype inthe sample. The individual or organization who determines the haplotypeneed not actually carry out the physical analysis of a sample from asubject; the haplotype can include information obtained by analysis ofthe sample by a third party. Thus the methods can include steps thatoccur at more than one site. For example, a sample can be obtained froma subject at a first site, such as at a health care provider or at thesubject's home in the case of a self-testing kit. The sample can beanalyzed at the same or a second site, e.g., at a laboratory, asequencing or genotyping facility, or other testing facility.Determining a haplotype can also include or consist of reviewing asubject's medical history or test results, where the medical history ortest results includes information regarding the identity, presence orabsence of one or more genetic markers in the subject.

Samples that are suitable for use in the methods described hereincontain genetic material, e.g., genomic DNA (gDNA). Non-limitingexamples of sources of samples include urine, blood, cells, and tissues.The sample itself will typically consist of nucleated cells (e.g., bloodor buccal cells), tissue, etc., removed from the subject. The subjectcan be an adult, a child, a fetus, or an embryo. In some embodiments,the sample is obtained prenatally, either from a fetus or an embryo orfrom the mother (e.g., from fetal or embryonic cells in the maternalcirculation). Methods and reagents are known in the art for obtaining,processing, and/or analyzing samples. In some embodiments, the sample isobtained with the assistance of a health care provider, e.g., to drawblood. In some embodiments, the sample is obtained without theassistance of a health care provider, e.g., where the sample is obtainednon-invasively, such as a sample comprising buccal cells that isobtained using a buccal swab or brush, or a mouthwash sample.

The sample may be further processed before the detecting step. Forexample, DNA in a cell or tissue sample can be separated from othercomponents of the sample. The sample can be concentrated and/or purifiedto isolate DNA. Cells can be harvested from a biological sample usingstandard techniques known in the art. For example, cells can beharvested by centrifuging a cell sample and resuspending the pelletedcells. The cells can be resuspended in a buffered solution such asphosphate-buffered saline (PBS). After centrifuging the cell suspensionto obtain a cell pellet, the cells can be lysed to extract DNA, e.g.,gDNA. See, e.g., Ausubel et al., 2003, supra. All samples obtained froma subject, including those subjected to any sort of further processing,are considered to be obtained from the subject.

SULT4A1-1 haplotype may be determined by any methods known in the art,e.g., gel electrophoresis, capillary electrophoresis, size exclusionchromatography, sequencing, and/or arrays to detect the presence orabsence of the marker(s) of the haplotype. Amplification of nucleicacids, where desirable, can be accomplished using methods known in theart, e.g., PCR.

Methods of nucleic acid analysis to detect polymorphisms and/orpolymorphic variants include, e.g., microarray analysis. Hybridizationmethods, such as Southern analysis, or fluorescent intensity analysis ofmicroarrays, can also be used (see Ausubel et al., 2003; Redon et al.,2006).

Other methods include direct manual sequencing (Church and Gilbert,1988; Sanger et al., 1977; U.S. Pat. No. 5,288,644); automatedfluorescent sequencing; single-stranded conformation polymorphism assays(SSCP); clamped denaturing gel electrophoresis (CDGE); two-dimensionalgel electrophoresis (2DGE or TDGE); conformational sensitive gelelectrophoresis (CSGE); denaturing gradient gel electrophoresis (DGGE)(Sheffield et al., 1989); mobility shift analysis (Orita et al., 1989);restriction enzyme analysis (Flavell et al., 1978; Geever et al., 1981);quantitative real-time PCR (Raca et al., 2004); heteroduplex analysis;chemical mismatch cleavage (CMC) (Cotton et al., 1985); RNase protectionassays (Myers et al., 1985); use of polypeptides that recognizenucleotide mismatches, e.g., E. coli mutS protein; allele-specific PCR.See, e.g., U.S. Patent Publication No. 2004/0014095, to Gerber et al.,which is incorporated herein by reference in its entirety. In someembodiments, the sequence is determined on both strands of DNA.

In order to detect polymorphisms and/or polymorphic variants, it willfrequently be desirable to amplify a portion of genomic DNA (gDNA)encompassing the polymorphic site. Such regions can be amplified andisolated by PCR using oligonucleotide primers designed based on genomicand/or cDNA sequences that flank the site. See e.g., PCR Primer: ALaboratory Manual; McPherson et al., 2000; Mattila et al., 1991; Eckertet al., 1991; and U.S. Pat. No. 4,683,202. Other amplification methodsthat may be employed include the ligase chain reaction (LCR) (Wu andWallace, 1989, Landegren et al., 1988), transcription amplification(Kwoh et al., 1989), self-sustained sequence replication (Guatelli etal., 1990), and nucleic acid based sequence amplification (NASBA).Guidelines for selecting primers for PCR amplification are well known inthe art. See, e.g., McPherson et al. (2000). A variety of computerprograms for designing primers are available, e.g., “Oligo” (NationalBiosciences, Inc, Plymouth Minn.), MacVector (Kodak/IBI), and the GCGsuite of sequence analysis programs (Genetics Computer Group, Madison,Wis. 53711).

In one example, a sample (e.g., a sample comprising genomic DNA), isobtained from a subject. The DNA in the sample is then examined todetermine a SULT4A1-1 haplotype as described herein. The haplotype canbe determined by any method described herein, e.g., by sequencing or byhybridization of the gene in the genomic DNA, RNA, or cDNA to a nucleicacid probe, e.g., a DNA probe (which includes cDNA and oligonucleotideprobes) or an RNA probe. The nucleic acid probe can be designed tospecifically or preferentially hybridize with a particular polymorphicvariant.

In some embodiments, a peptide nucleic acid (PNA) probe can be usedinstead of a nucleic acid probe in the hybridization methods describedabove. PNA is a DNA mimetic with a peptide-like, inorganic backbone,e.g., N-(2-aminoethyl)glycine units, with an organic base (A, G, C, T orU) attached to the glycine nitrogen via a methylene carbonyl linker(see, e.g., Nielsen et al., 1994). The PNA probe can be designed tospecifically hybridize to a nucleic acid comprising a polymorphicvariant of the SULT4A1-1 haplotype.

In some embodiments, restriction digest analysis can be used to detectthe existence of a polymorphic variant of a polymorphism, if alternatepolymorphic variants of the polymorphism result in the creation orelimination of a restriction site. A sample containing genomic DNA isobtained from the individual. Polymerase chain reaction (PCR) can beused to amplify a region comprising the polymorphic site, andrestriction fragment length polymorphism analysis is conducted (seeAusubel et al., supra). The digestion pattern of the relevant DNAfragment may indicate the presence or absence of a particularpolymorphic variant of the SULT4A1 polymorphism and may be thereforeindicative of the presence or absence of the SULT4A1-1 haplotype.

Sequence analysis can also be used to detect specific polymorphicvariants. A sample comprising DNA or RNA is obtained from the subject.PCR or other appropriate methods can be used to amplify a portionencompassing the polymorphic site, if desired. The sequence is thenascertained, using any standard method, and the presence of apolymorphic variant is determined.

DNA containing the amplified portion may be dot-blotted, using standardmethods (see Ausubel et al., supra), and the blot contacted with theoligonucleotide probe. The presence of specific hybridization of theprobe to the DNA is then detected. Specific hybridization of anallele-specific oligonucleotide probe (specific for a polymorphicvariant indicative of susceptibility to altered pharmacological responseor endophenotype) to DNA from the subject may determine a SULT4A1-1haplotype.

Allele-specific oligonucleotides can be used to detect the presence of apolymorphic variant, e.g., through the use of dot-blot hybridization ofamplified oligonucleotides with allele-specific oligonucleotide (ASO)probes (see, for example, Saiki et al., 1986). An “allele-specificoligonucleotide” (also referred to herein as an “allele-specificoligonucleotide probe”) is typically an oligonucleotide of approximately10-50 base pairs, preferably approximately 15-30 base pairs, thatspecifically hybridizes to a nucleic acid region that contains apolymorphism. An allele-specific oligonucleotide probe that is specificfor a particular polymorphism can be prepared using standard methods(see Ausubel et al., supra).

In some embodiments, fluorescence polarization template-directeddye-terminator incorporation (FP-TDI) is used to determine which ofmultiple polymorphic variants of a polymorphism is present in a subject(Chen et al., 1999). Rather than involving use of allele-specific probesor primers, this method employs primers that terminate adjacent to apolymorphic site, so that extension of the primer by a single nucleotideresults in incorporation of a nucleotide complementary to thepolymorphic variant at the polymorphic site.

Real-time pyrophosphate DNA sequencing is yet another approach todetection of polymorphisms and polymorphic variants (Alderborn et al.,2000). Additional methods include, for example, PCR amplification incombination with denaturing high performance liquid chromatography(dHPLC) (Underhill et al., 1997).

The methods can include determining the genotype of a subject withrespect to both copies of the polymorphic site present in the genome.For example, the complete genotype may be characterized as −/−, as +/+,or as +/+, where a plus sign indicates the presence of the polymorphicvariant of interest, such as rs2285162(A), rs2285166(T), orrs2285167(G), and a minus sign indicates the absence of the polymorphicvariant of interest and/or the presence of the other or wild typesequence at the polymorphic site. If multiple polymorphic variants existat a site, this can be appropriately indicated by specifying which onesare present in the subject. Any of the detection means described hereincan be used to determine the genotype of a subject with respect to oneor both copies of the polymorphism present in the subject's genome.

In some embodiments, it is desirable to employ methods that can detectthe presence of multiple polymorphisms (e.g., polymorphic variants at aplurality of polymorphic sites) in parallel or substantiallysimultaneously. Oligonucleotide arrays represent one suitable means fordoing so. Other methods, including methods in which reactions (e.g.,amplification, hybridization) are performed in individual vessels, e.g.,within individual wells of a multi-well plate or other vessel may alsobe performed so as to detect the presence of multiple polymorphicvariants (e.g., polymorphic variants at a plurality of polymorphicsites) in parallel or substantially simultaneously according to certainembodiments of the invention.

IV. Psychotic Disorders

Certain aspects of the invention involve using the SULT4A1-1 haplotypestatus to optimize treatments for psychotic disorders, such asschizophrenia (SZ), schizotypal personality disorder (SPD),schizoaffective disorder (SD), and/or bipolar disorders (BD).

Schizophrenia and bipolar disorder are life-long, severely disablingmental illnesses. The clinical criteria for these neuropsychiatricillnesses have continued to evolve through a consensus process organizedby the American Psychiatric Association (APA) and published in itsDiagnostic and Statistical Manual (DSM) I-IV (American PsychiatricAssoc. Diagostic and Statistical Manual of Mental Disorders, 1994). Theinventors disclose here some of the key features of both illnesses ascurrently conceived, with the full awareness that there is strongevidence for overlap between these disorders in genetic risk factors andresponse to treatment. Nevertheless, all indications are that DSM-V,which is currently being developed by the APA, will maintain thisdistinction more or less in the current form. Also because FDAindications for treatment have been and may continue to be given fordrugs for each disorder separately, having genetic information whichpertains to classification and prediction of response to treatment is ofconsiderable value.

Schizophrenia and bipolar disorder share some common clinical featureswhile differing on others. Schizophrenia is characterized by psychoticsymptoms (delusions, hallucinations), disorganized thinking andcognitive impairment and poor social and work function. Additionally,some schizophrenia patients can have severe negative symptoms, includingblunted affect and social and emotional withdrawal. Bipolar Disorder ischaracterized by two main types of mood disturbances, with depressionbeing the most common type and mania, or hypomania less frequent.Psychotic disorders may be present in either the manic or depressivemood phases. Both disorders have a high risk for suicide attempts andcompletions.

Schizophrenia usually begins in the late teens and early 20's. Itaffects about 1% of the population. Conversely, bipolar disorder mostoften occurs in the 3^(rd) and 4^(th) decades of life. Bipolar (BP) TypeI affects about 1.5% of the population. BP type II and BP Not OtherwiseSpecified (NOS) afflict another 2-4% of the population. Life-long drugtreatment is often required to minimize the number of acute episodes,the need for hospitalization or assisted living, and to optimize dailyfunctioning. Suicide occurs in 5% of schizophrenia cases and 10% ofbipolar disorder cases. Patients with schizophrenia or bipolar disordercan have “acute” episodes which are characterized by abrupt and largeincreases in psychotic symptoms. Often, these episodes occur after aperiod of non-compliance with medication. Both are generally treatedwith one or more classes of psychotropic medications. Atypicalantipsychotic drugs treat psychosis and mood disturbances. Additionally,mood stabilizers such as lithium or valproate treat the manic phase ofbipolar disorder, and antidepressants and atypical antipsychotic drugstarget the depressive phase. Antipsychotics and mood stabilizers areoften used together for “maintenance” treatment to prevent relapse.

A. Schizophrenia (SZ)

SZ is considered a clinical syndrome, and is probably a constellation ofseveral pathologies. Substantial heterogeneity is seen between cases;this is thought to reflect multiple overlapping etiologic factors,including both genetic and environmental contributions. A diagnosis ofSZ is typically indicated by chronic psychotic symptoms, e.g.,hallucinations and delusions. Disorganization of thought and behaviorare common and are considered distinguishing factors in the diagnosis ofSZ. Patients typically have some subtle impairments in cognition.Reduced emotional experience and expression, low drive, and impairedspeech are observed in a subgroup of patients. Cognitive, emotional andsocial impairments often appear early in life, while the psychoticsymptoms typically manifest in late adolescence or early adulthood inmen, a little later in women.

A diagnosis of SZ can be made according to the criteria reported in theDiagnostic and Statistical Manual of Mental Disorders, Fourth Edition,Text Revision, American Psychiatric Association, 2000 (referred toherein as DSM-IV) as follows:

Diagnostic Criteria for SZ—All six criteria must be met for a diagnosisof SZ.

A. Characteristic symptoms: Two (or more) of the following, each presentfor a significant portion of time during a one month period (or less ifsuccessfully treated):

(1) delusions; (2) hallucinations; (3) disorganized speech (e.g.,frequent derailment or incoherence); (4) grossly disorganized orcatatonic behavior; (5) negative symptoms, e.g., affective flattening,alogia, or avolition.

Only one criterion A symptom is required if delusions are bizarre orhallucinations consist of a voice keeping up a running commentary on theperson's behavior or thoughts, or two or more voices conversing witheach other.

B. Social/occupational dysfunction: For a significant portion of thetime since the onset of the disturbance, one or more major areas offunctioning such as work, interpersonal relations, or self-care aremarkedly below the level achieved prior to the onset (or when the onsetis in childhood or adolescence, failure to achieve expected level ofinterpersonal, academic, or occupational achievement).

C. Duration: Continuous signs of the disturbance persist for at least 6months. This 6-month period must include at least 1 month of symptoms(or less if successfully treated) that meet Criterion A (i.e.,active-phase symptoms) and may include periods of prodromal or residualsymptoms. During these prodromal or residual periods, the signs of thedisturbance may be manifested by only negative symptoms or two or moresymptoms listed in Criterion A present in an attenuated form (e.g., oddbeliefs, unusual perceptual experiences).

D. Schizoaffective and Mood Disorder Exclusion: Schizoaffective Disorderand Mood Disorder With Psychotic Features have been ruled out becauseeither (1) no major depressive, manic, or mixed episodes have occurredconcurrently with the active-phase symptoms; or (2) if mood episodeshave occurred during active-phase symptoms, their total duration hasbeen brief relative to the duration of the active and residual periods.

E. Substance/General Medical Condition Exclusion: The disturbance is notdue to the direct physiological effects of a substance (e.g., a drug ofabuse, a medication) or a general medical condition.

F. Relationship to a Pervasive Developmental Disorder: If the patienthas a history of Autistic Disorder or another Pervasive DevelopmentalDisorder, the additional diagnosis of SZ is made only if prominentdelusions or hallucinations are also present for at least a month (orless if successfully treated).

B. Schizoaffective Disorder (SD)

SD is characterized by the presence of affective (depressive or manic)symptoms and schizophrenic symptoms within the same, uninterruptedepisode of illness.

The DSM-IV Criteria for a diagnosis of schizoaffective disorder is asfollows:

An uninterrupted period of illness during which, at some time, there iseither (1) a Major Depressive Episode (which must include depressedmood), (2) a Manic Episode, or (3) a Mixed Episode, concurrent withsymptoms that meet (4) Criterion A for SZ, above.

A. Criteria for Major Depressive Episode

At least five of the following symptoms must be present during the same2-week period and represent a change from previous functioning; at leastone of the symptoms is either (1) depressed mood or (2) loss of interestor pleasure.

(1) depressed mood most of the day, nearly every day, as indicated byeither subjective report (e.g., feels sad or empty) or observation madeby others (e.g., appears tearful). In children and adolescents, this canbe an irritable mood.

(2) markedly diminished interest or pleasure in all, or almost all,activities most of the day, nearly every day (as indicated by eithersubjective account or observation made by others)

(3) significant weight loss when not dieting or weight gain (e.g., achange of more than 5% of body weight in a month), or decrease orincrease in appetite nearly every day. (In children, failure to makeexpected weight gains is considered).

(4) insomnia or hypersomnia nearly every day

(5) psychomotor agitation or retardation nearly every day (observable byothers, not merely subjective feelings of restlessness or being sloweddown)

(6) fatigue or loss of energy nearly every day

(7) feelings of worthlessness or excessive or inappropriate guilt (whichmay be delusional) nearly every day (not merely self-reproach or guiltabout being sick)

(8) diminished ability to think or concentrate, or indecisiveness,nearly every day

(either by subjective account or as observed by others)

(9) recurrent thoughts of death (not just fear of dying), recurrentsuicidal ideation without a specific plan, or a suicide attempt or aspecific plan for committing suicide

In addition, the symptoms do not meet criteria for a Mixed Episode. Thesymptoms cause clinically significant distress or impairment in social,occupational, or other important areas of functioning. The symptoms arenot due to the direct physiological effects of a substance (e.g., a drugof abuse, a medication) or a general medical condition (e.g.,hypothyroidism).

The symptoms are not better accounted for by Bereavement, i.e., afterthe loss of a loved one, the symptoms persist for longer than 2 months,or are characterized by marked functional impairment, morbidpreoccupation with worthlessness, suicidal ideation, psychotic symptoms,or psychomotor retardation.

B. Criteria for Manic Episode

A manic episode is a distinct period of abnormally and persistentlyelevated, expansive, or irritable mood, lasting at least one week (orany duration, if hospitalization is necessary).

During the period of mood disturbance, three (or more) of the followingsymptoms have persisted (four if the mood is only irritable) and havebeen present to a significant degree:

(1) inflated self-esteem or grandiosity

(2) decreased need for sleep (e.g., feels rested after only 3 hours ofsleep)

(3) more talkative than usual or pressure to keep talking

(4) flight of ideas or subjective experience that thoughts are racing

(5) distractibility (i.e., attention too easily drawn to unimportant orirrelevant external stimuli)

(6) increase in goal-directed activity (either socially, at work orschool, or sexually) or psychomotor agitation

(7) excessive involvement in pleasurable activities that have a highpotential for painful consequences (e.g., engaging in unrestrainedbuying sprees, sexual indiscretions, or foolish business investments)

The symptoms do not meet criteria for a Mixed Episode. The mooddisturbance is sufficiently severe to cause marked impairment inoccupational functioning or in usual social activities or relationshipswith others, or to necessitate hospitalization to prevent harm to selfor others, or there are psychotic features. The symptoms are not due tothe direct physiological effects of a substance (e.g., a drug of abuse,a medication, or other treatment) or a general medical condition (e.g.,hyperthyroidism).

C. Criteria for Mixed Episode

A mixed episode occurs when the criteria are met both for a ManicEpisode and for a Major Depressive Episode (except for duration) nearlyevery day during at least a 1-week period. The mood disturbance issufficiently severe to cause marked impairment in occupationalfunctioning or in usual social activities or relationships with others,or to necessitate hospitalization to prevent harm to self or others, orthere are psychotic features.

The symptoms are not due to the direct physiological effects of asubstance (e.g., a drug of abuse, a medication, or other treatment) or ageneral medical condition (e.g., hyperthyroidism).

D. Criterion A of SZ

See above.

E. Types of SD

The type of SD may be may be specifiable, as either Bipolar Type, if thedisturbance includes a Manic or a Mixed Episode (or a Manic or a MixedEpisode and Major Depressive Episodes), or Depressive Type, if thedisturbance only includes Major Depressive Episodes.

F. Associated Features

Features associated with SD include Learning Problems, Hypoactivity,Psychotic, Euphoric Mood, Depressed Mood, Somatic/Sexual Dysfunction,Hyperactivity, Guilt/Obsession, Odd/Eccentric/Suspicious Personality,Anxious/Fearful/Dependent Personality, and Dramatic/Erratic/AntisocialPersonality.

C. Schizotypal Personality Disorder (SPD)

A diagnosis of SPD under the criteria of the DSM-IV is generally basedon a pervasive pattern of social and interpersonal deficits marked byacute discomfort with, and reduced capacity for, close relationships aswell as by cognitive or perceptual distortions and eccentricities ofbehavior, beginning by early adulthood and present in a variety ofcontexts, as indicated by five (or more) of the following:

(1) ideas of reference (excluding delusions of reference)

(2) odd beliefs or magical thinking that influences behavior

(3) inconsistent with subcultural norms (e.g., superstitiousness, beliefin clairvoyance, telepathy, or “sixth sense” in children andadolescents, bizarre fantasies or preoccupations)

(4) unusual perceptual experiences, including bodily illusions

(5) odd thinking and speech (e.g., vague, circumstantial, metaphorical,overelaborate, or stereotyped)

(6) suspiciousness or paranoid ideation

(7) inappropriate or constricted affect

(8) behavior or appearance that is odd, eccentric, or peculiar

(9) lack of close friends or confidants other than first-degreerelatives

(10) excessive social anxiety that does not diminish with familiarityand tends to be associated with paranoid fears rather than negativejudgments about self

SPD is diagnosed if the symptoms do not occur exclusively during thecourse of SZ, a Mood Disorder With Psychotic Features, another PsychoticDisorder, or a Pervasive Developmental Disorder, and the disturbance isnot due to the direct physiological effects of a substance (e.g., a drugof abuse, a medication) or a general medical condition.

Associated features of SPD include Depressed Mood andOdd/Eccentric/Suspicious Personality.

D. Bipolar Disorder (BD)

Bipolar disorder is also known as manic-depression or manic-depressivedisorder. This condition is characterized by mood that alternatesbetween two emotional extremes, or poles: the sadness of depression andthe euphoria of mania (see symptoms of mania below).

Between these emotional swings, there are periods when a person's moodis quite normal. When a person is in the depressed phase of bipolarillness, he or she will have the same symptoms as those found in majordepressive disorder. The depressive episodes can often be severe. Whilein a manic phase, a person experiences mood that is extremely elevated,expansive, or irritable. Mania can seriously impair one's normaljudgment. When manic, a person is prone towards reckless andinappropriate behavior such as engaging in wild spending sprees orhaving promiscuous sex. He or she may not be able to realize the harm ofhis/her behavior and may even lose touch with reality.

There are two primary types of bipolar disorder:

Bipolar I Disorder is diagnosed when a person has had at least one manicor mixed episode, often along with a major depressive episode. Itaffects equal numbers of men and women in approximately 0.4% to 1.6% ofthe population.

Bipolar II Disorder is diagnosed when a person has had a majordepressive episode along with at least one hypomanic episode. It affectsmore women than men in about 0.5% of the population.

People with bipolar disorder experience a wide range of feelingsdepending on the phase of the illness is present. During a phase ofdepression, a person will have many of the symptoms of a majordepressive episode. He or she may have despondent mood, a loss ofenergy, feelings of worthlessness or guilt, or problems withconcentration. Thoughts of suicide are not uncommon. In fact, 10% to 15%of those with bipolar disorder may die by suicide. If the depression issevere, a person may need to be hospitalized for his or her own safety.For those who go through a phase of hypomania, the experience usuallyfeels quite good. If a person's mood and spirit lightens, he or she willbe more outgoing and notice more energy and enhanced self-esteem. Lotsof ideas come with ease and a person may feel compelled towards greateractivity and productivity. A person in a hypomanic phase may also feelmore powerful and omnipotent.

The manic phase is the most extreme part of bipolar disorder. A personbecomes euphoric, ideas come much too fast, and concentration is nearlyimpossible. Anger, irritability, fear, and a sense of being out ofcontrol are overwhelming. A person's judgment is impaired, and he or shemay behave recklessly without a sense of consequence. Some people losetouch with reality and experience delusions and hallucinations. Whenthis happens, people often need to be hospitalized for their own safety.If a person with bipolar disorder experiences a severe manic episode, heor she may be abusive to children, spouses, or engage in other violentbehaviors. There may also be problems with attendance and performance atschool or work, as well as significant difficulties in personalrelationships.

The cycles of bipolar disorder may be different for each person.Oftentimes a person may first experience depression. Then depression maybe replaced with manic symptoms and the cycle between depression andmania may continue for days, weeks, or months. Between phases ofdepression and mania some people return to their normal mood. Someothers have several periods of either depression or mania. Still othersmay experience several bouts of depression with infrequent phases ofhypomania, or repeated manic episodes with occasional depressiveperiods. A portion of people, roughly 10% to 20% may only experiencemania, while others can have both depression and mania at the same time.

For at least 90% of those who have bipolar disorder the condition isrecurrent. They will experience future symptoms of the cycles of maniaand depression. Approximately 60%-70% of manic episodes may happen justbefore or after a depressive episode, and this pattern may happen in aparticular way for each person. Most people return to a regular level offunctioning between episodes, while some (about 20%-30%) may continue tohave some problems with mood stability and social and occupationalfunctioning.

Bipolar I disorder affects equal numbers of males and females; however,there does appear to be a gender difference in the onset of the illness.Females are more likely to experience a first episode of depression,while males tend to have a first episode that is manic. Women who havebipolar I or II disorder and who have children may be at a higher riskof experiencing bipolar episodes within several months of giving birth.

A first episode of mania is most likely to occur when a person is inhis/her teens or twenties. If a person develops bipolar disorder for thefirst time after 40 years of age, he or she should be evaluated for thepossibility of a medical illness or substance use.

People who have immediate relatives with bipolar I disorder have ahigher risk of developing a mood disorder themselves. For these peoplethe rate of developing bipolar II disorder or major depression is 4%-24%and bipolar I disorder is 1%-5%.

Of adolescents who have recurrent major depressive episodes, about10%-15% of them will likely develop bipolar disorder.

Diagnostic Criteria of Bipolar I Disorder

Summarized from the Diagnostic and Statistical Manual of MentalDisorders-Fourth Edition

A. A person experiences a current or recent episode that is manic,hypomanic, mixed, or depressed.

To be a manic episode, for at least one week a person's mood must be outof the ordinary and continuously heightened, exaggerated, or irritable.

At least three of the following seven symptoms have been significant andenduring. If the mood is only irritable, then four symptoms arerequired.

Self-esteem is excessive or grandiose.

The need for sleep is greatly reduced.

Talks much more than usual.

Thoughts and ideas are continuous and without a pattern or focus.

Easily distracted by unimportant things.

An increase in purposeful activity or productivity, or behaving andfeeling agitated.

Reckless participation in enjoyable activities that create a high riskfor negative consequences (e.g., extensive spending sprees, sexualpromiscuity).

The persons' symptoms do not indicate a mixed episode.

The person's symptoms are a cause of great distress or difficulty infunctioning at home, work, or other important areas. Or, the symptomsrequire the person to be hospitalized to protect the person from harminghimself/herself or others. Or, the symptoms include psychotic features(hallucinations, delusions).

The person's symptoms are not caused by substance use (e.g., alcohol,drugs, medication), or a medical disorder.

B. Unless this is a first single manic episode there has been at leastone manic, mixed, hypomanic, or depressive episode.

For a major depressive episode a person must have experienced at leastfive of the nine symptoms below for the same two weeks or more, for mostof the time almost every day, and this is a change from his/her priorlevel of functioning. One of the symptoms must be either (a) depressedmood, or (b) loss of interest.

Depressed mood. For children and adolescents, this may be irritablemood.

A significantly reduced level of interest or pleasure in most or allactivities.

A considerable loss or gain of weight (e.g., 5% or more change of weightin a month when not dieting). This may also be an increase or decreasein appetite. For children, they may not gain an expected amount ofweight.

Difficulty falling or staying asleep (insomnia), or sleeping more thanusual (hypersomnia).

Behavior that is agitated or slowed down. Others should be able toobserve this.

Feeling fatigued, or diminished energy.

Thoughts of worthlessness or extreme guilt (not about being ill).

Ability to think, concentrate, or make decisions is reduced.

Frequent thoughts of death or suicide (with or without a specific plan),or attempt of suicide.

The persons' symptoms do not indicate a mixed episode.

The person's symptoms are a cause of great distress or difficulty infunctioning at home, work, or other important areas.

The person's symptoms are not caused by substance use (e.g., alcohol,drugs, medication), or a medical disorder.

The person's symptoms are not due to normal grief or bereavement overthe death of a loved one, they continue for more than two months, orthey include great difficulty in functioning, frequent thoughts ofworthlessness, thoughts of suicide, symptoms that are psychotic, orbehavior that is slowed down (psychomotor retardation).

C. Another disorder does not better explain the episode.

Diagnostic Criteria of Bipolar II Disorder

Summarized from the Diagnostic and Statistical Manual of MentalDisorders-Fourth Edition

A. The person currently has, or in the past has had at least one majordepressive episode:

For a major depressive episode a person must have experienced at leastfive of the nine symptoms below for the same two weeks or more, for mostof the time almost every day, and this is a change from his/her priorlevel of functioning. One of the symptoms must be either (a) depressedmood, or (b) loss of interest.

Depressed mood. For children and adolescents, this may be irritablemood.

A significantly reduced level of interest or pleasure in most or allactivities.

A considerable loss or gain of weight (e.g., 5% or more change of weightin a month when not dieting). This may also be an increase or decreasein appetite. For children, they may not gain an expected amount ofweight.

Difficulty falling or staying asleep (insomnia), or sleeping more thanusual (hypersomnia).

Behavior that is agitated or slowed down. Others should be able toobserve this.

Feeling fatigued, or diminished energy.

Thoughts of worthlessness or extreme guilt (not about being ill).

Ability to think, concentrate, or make decisions is reduced.

Frequent thoughts of death or suicide (with or without a specific plan),or attempt of suicide.

The persons' symptoms do not indicate a mixed episode.

The person's symptoms are a cause of great distress or difficulty infunctioning at home, work, or other important areas.

The person's symptoms are not caused by substance use (e.g., alcohol,drugs, medication), or a medical disorder.

The person's symptoms are not due to normal grief or bereavement overthe death of a loved one, they continue for more than two months, orthey include great difficulty in functioning, frequent thoughts ofworthlessness, thoughts of suicide, symptoms that are psychotic, orbehavior that is slowed down (psychomotor retardation).

B. The person currently has, or in the past has had at least onehypomanic episode:

For a hypomanic episode a person's mood must be out of the ordinary andcontinuously heightened, exaggerated, or irritable for at least fourdays.

At least three of the following seven symptoms have been significant andenduring. If the mood is only irritable, then four symptoms arerequired.

Self-esteem is excessive or grandiose.

The need for sleep is greatly reduced.

Talks much more than usual.

Thoughts and ideas are continuous and without a pattern or focus.

Easily distracted by unimportant things.

An increase in purposeful activity or productivity, or behaving andfeeling agitated.

Reckless participation in enjoyable activities that create a high riskfor negative consequences (e.g., extensive spending sprees, sexualpromiscuity).

The episode is a substantial change for the person and uncharacteristicof his or her usual functioning.

The changes of functioning and mood can be observed by others.

The person's symptoms are NOT severe enough to cause difficulty infunctioning at home, work, or other important areas. Also, the symptomsneither require the person to be hospitalized, nor are there anypsychotic features.

The person's symptoms are not caused by substance use (e.g., alcohol,drugs, medication), or a medical disorder. C. The person has neverexperienced a manic or mixed episode. D. Another disorder does notbetter explain the episode. E. The symptoms are a cause of greatdistress or difficulty in functioning at home, work, or other importantareas.

E. Psychiatric Endophenotypes in SZ

A number of endophenotypes, i.e., intermediate phenotypes, that may moreclosely reflect biological mechanisms behind SZ, have been suggested,such as prepulse inhibition, structural abnormalities evident in MRIscans, specific domains of cognition (e.g., executive function), finemotor performance, working memory, etc.

Endophenotypes can also include clinical manifestations such ashallucinations, paranoia, mania, depression, obsessive-compulsivesymptoms, etc., as well as response or lack of response to drugs andcomorbidity for substance and alcohol abuse. See, e.g., Kendler et al.(1995); Gottesman and Gould (2003); Cadenhead, 2002; Gottesman and Gould(2003); Heinrichs (2004); and Zobel and Maier (2004). There is nowevidence that some candidate genes that were identified using DSM-IVtype categorical definitions for “affected” individuals may influencespecific endophenotypes, see, e.g., Baker et al. (2005); Cannon et al.(2005); Gothelf et al. (2005); Hallmayer et al. (2005); Callicott et al.(2005); Gornick et al. (2005).

F. Use of PANSS (Positive and Negative Syndrome Scale) score fordifferential Diagnosis and Evaluation of Clinical Response

The Positive and Negative Syndrome Scale (PANSS) is a comprehensivepsychometric scale used to classify psychopathology for severeneuropsychiatric diseases, including SZ and BD. It measures a number ofpsychiatric endophenotypes or dimensions using quantitative scales basedon the scoring of patients by clinicians. It is widely used to classifypatients into specific subtypes, and is commonly used for measuring theimprovement of symptoms in response to clinical interventions (Kay etal., 1987; Kay et al., 1989; Leucht et al., 2005).

Detailed information on PANSS and Scoring Criteria can be found in theart, e.g., on the world wide web at panss.org, or in the book by Kay(1991) which is incorporated herein in its entirety by reference. Basedon these sources, the methodology is summarized briefly below.

PANSS comprises 30 individual subscales. Seven constitute a PositiveSymptom Scale, seven the Negative Symptom Scale, and the remaining 16items make up a General Psychopathology Scale. The scores for thesescales are arrived at by summation of ratings across component items.Therefore, the potential ranges are 7 to 49 for the Positive andNegative Scales, and 16 to 112 for the General Psychopathology Scale(Source: The PANSS Institute).

Each of the 30 items is accompanied by a specific definition as well asdetailed anchoring criteria for all seven rating points. These sevenpoints represent increasing levels of psychopathology, as follows:

1—absent

2—minimal

3—mild

4—moderate

5—moderate severe

6—severe

7—extreme

The PANSS Individual subscales are described below.

P1. DELUSIONS—Beliefs which are unfounded, unrealistic andidiosyncratic.

P2. CONCEPTUAL DISORGANIZATION—Disorganized process of thinkingcharacterized by disruption of goal-directed sequencing, e.g.,circumstantiality, loose associations, tangentiality, gross illogicalityor thought block.

P3. HALLUCINATORY BEHAVIOUR—Verbal report or behaviour indicatingperceptions which are not generated by external stimuli. These may occurin the auditory, visual, olfactory or somatic realms.

P4. EXCITEMENT—Hyperactivity as reflected in accelerated motorbehaviour, heightened responsivity to stimuli, hypervigilance orexcessive mood lability.

P5. GRANDIOSITY—Exaggerated self-opinion and unrealistic convictions ofsuperiority, including delusions of extraordinary abilities, wealth,knowledge, frame, power and moral righteousness.

P6. SUSPICIOUSNESS/PERSECUTION—Unrealistic or exaggerated ideas ofpersecution, as reflected in guardedness, ad distrustful attitude,suspicious hypervigilance or frank delusions that others mean harm.

P7. HOSTILITY—Verbal and nonverbal expressions of anger and resentment,including sarcasm, passive-aggressive behavior, verbal abuse andassualtiveness.

N1. BLUNTED AFFECT—Diminished emotional responsiveness as characterizedby a reduction in facial expression, modulation of feelings andcommunicative gestures.

N2. EMOTIONAL WITHDRAWAL—Lack of interest in, involvement with, andaffective commitment to life's events.

N3. POOR RAPPORT—Lack of interpersonal empathy, openness in conversationand sense of closeness, interest or involvement with the interviewer.This is evidenced by interpersonal distancing and reduced verbal andnonverbal communication.

N4. PASSIVE/APATHETIC SOClAL WITHDRAWAL—Diminished interest andinitiative in social interactions due to passivity, apathy, anergy oravolition. This leads to reduced interpersonal involvements and neglectof activities of daily living.

N5. DIFFICULTY IN ABSTRACT THINKING—Impairment in the use of theabstract-symbolic mode of thinking, as evidenced by difficulty inclassification, forming generalizations and proceeding beyond concreteor egocentric thinking in problem-solving tasks.

N6. LACK OF SPONTANEITY AND FLOW OF CONVERSATION—Reduction in the normalflow of communication associated with apathy, avolition, defensivenessor cognitive deficit. This is manifested by diminished fluidity andproductivity of the verbal interactional process.

N7. STEREOTYPED THINKING—Decreased fluidity, spontaneity and flexibilityof thinking, as evidenced in rigid, repetitious or barren thoughtcontent.

G1. SOMATIC CONCERN—Physical complaints or beliefs about bodily illnessor malfunctions. This may range from a vague sense of ill being toclear-cut delusions of catastrophic physical disease.

G2. ANXIETY—Subjective experience of nervousness, worry, apprehension orrestlessness, ranging from excessive concern about the present or futureto feelings of panic.

G3. GUILT FEELINGS—Sense of remorse or self-blame for real or imaginedmisdeeds in the past.

G4. TENSION—Overt physical manifestations of fear, anxiety, andagitation, such as stiffness, tremor, profuse sweating and restlessness.

G5. MANNERISMS AND POSTURING—Unnatural movements or posture ascharacterized be an awkward, stilted, disorganized, or bizarreappearance.

G6. DEPRESSION—Feelings of sadness, discouragement, helplessness andpessimism.

G7. MOTOR RETARDATION—Reduction in motor activity as reflected inslowing or lessening or movements and speech, diminished responsivenessof stimuli, and reduced body tone.

G8. UNCOOPERATIVENESS—Active refusal to comply with the will ofsignificant others, including the interviewer, hospital staff or family,which may be associated with distrust, defensiveness, stubbornness,negativism, rejection of authority, hostility or belligerence.

G9. UNUSUAL THOUGHT CONTENT—Thinking characterized by strange, fantasticor bizarre ideas, ranging from those which are remote or atypical tothose which are distorted, illogical and patently absurd.

G10. DISORIENTATION—Lack of awareness of one's relationship to themilieu, including persons, place and time, which may be due to confusionor withdrawal.

G11. POOR ATTENTION—Failure in focused alertness manifested by poorconcentration, distractibility from internal and external stimuli, anddifficulty in harnessing, sustaining or shifting focus to new stimuli.

G12. LACK OF JUDGMENT AND INSIGHT—Impaired awareness or understanding ofone's own psychiatric condition and life situation. This is evidenced byfailure to recognize past or present psychiatric illness or symptoms,denial of need for psychiatric hospitalization or treatment, decisionscharacterized by poor anticipation or consequences, and unrealisticshort-term and long-range planning

G13. DISTURBANCE OF VOLITION—Disturbance in the willful initiation,sustenance and control of one's thoughts, behavior, movements andspeech.

G14. POOR IMPULSE CONTROL—Disordered regulation and control of action oninner urges, resulting in sudden, unmodulated, arbitrary or misdirecteddischarge of tension and emotions without concern about consequences.

G15. PREOCCUPATION—Absorption with internally generated thoughts andfeelings and with autistic experiences to the detriment of realityorientation and adaptive behavior.

G16. ACTIVE SOClAL AVOIDANCE—Diminished social involvement associatedwith unwarranted fear, hostility, or distrust.

Each patient's disease manifestation and process is unique. PANSSprovides a structured, objective way of describing the various aspectsof psychopathology of a given patient. However, proper implementation ofthe PANSS requires highly trained personnel to conduct the assessmentand to interpret the results, and there is potential for site to sitevariability, especially outside the research setting.

Each of the PANSS composite scales and subscales can be considered aclinical endophenotype. The ability to link genetic profiles to theseclinical endophenotypes changes as response to psychotic treatments, orseverity of the diseases, will enable clinicians to refine a patient'sdiagnosis and develop a personalized therapeutic strategy for eachpatient. By identifying the genetic contributions to specificendophenotypes, the physician can create a personalized diagnosis andtreatment regime for the patient.

Additionally, changes in PANSS or the Brief Psychiatric Rating Scale(BPRS), which is derived from PANSS, are often the primary measures ofefficacy in clinical trials. One commonly accepted measure of positiveclinical response is a decrease of >20% in total PANSS or BPRS.Moreover, certain subscales and composite scores are also evaluated forchange. For example, positive symptoms and negative symptoms are twocomposite scores that have clinical relevance.

G. Clinical Global Impressions (CGI) Scale

The CATIE clinical data set included the Clinical Global Impression(CGI) Scale, an observer-provided assessment of the psychiatric healthof the patient (Stroup et al., 2003; Guy 1976). Patients are rated withthe CGI Scale from 1 to 7, with higher scores indicating greaterseverity of illness. The CATIE study provided a response variable thatmeasured the time (in months) of successful treatment as measured by theCGI scale (“TMSUCC1” in the CATIE data).

The Clinical Global Impression (CGI) Scale is a three item observer-ratescale that measures illness severity (CGIS), global improvement orchange (CGIC), and therapeutic response. (Guy 1976). One of the mostwidely-used formats is the Early Clinical Drug Evaluation Programversion of the CGI. This format asks a clinician to rate the patientrelative to their past experience with other patients with the samediagnosis. This may be done with or without collateral information. TheCGI has proven to be a strong measure of efficacy in many clinical drugtrials. It is also quick and easy to administer.

Under the CGI, each component is separately rated on a 7-point scale. Onthe CGIS scale, which measures the severity of illness, the responsesrange from 1 (normal) to 7 (amongst the most severely ill patients). Onthe CGIC scale, which measures global improvement or change, theresponses range from 1 (very much improved) to 7 (very much worse).Treatment response ratings take into account both therapeutic effect andtreatment-related adverse events (side effects). The treatment responseratings may range from 0 (marked improvement and no side-effects) and 4(unchanged or worse and side-effects outweigh the therapeutic effects).The CGI scale does not produce a global score, but rather rates eachcomponent separately.

An example of the Early Clinical Drug Evaluation Program version of theCGI system is found below (Reproduced from Guy W, editor. ECDEUAssessment Manual for Psychopharmacology. 1976. Rockville, Md., U.S.Department of Health, Education, and Welfare):

1. Severity of illness: Considering your total clinical experience withthis particular population, how mentally ill is the patient at thistime?

0=Not assessed

1=Normal, not at all ill

2=Borderline mentally ill

3=Mildly ill

4=Moderately ill

5=Markedly ill

6=Severely ill

7=Among the most extremely ill patients

2. Global improvement: Rate total improvement whether or not, in yourjudgment, it is due entirely to drug treatment. Compared to hiscondition at admission to the project, how much has he changed?

0=Not assessed

1=Very much improved

2=Much improved

3=Minimally improved

4=No change

5=Minimally worse

6=Much worse

7=Very much worse

3. Efficacy index: Rate this item on the basis of drug effect only.Select the terms which best describe the degrees of therapeutic effectand side effects and record the number in the box where the two itemsintersect. EXAMPLE: Therapeutic effect is rated as ‘Moderate’ and sideeffects are judged ‘Do not significantly interfere with patient'sfunctioning’=06

Side effects Do not Out- significantly Significantly weighs interferewith interferes with thera- patient's patient's peutic Therapeuticeffect None functioning functioning effect Marked Vast 01 02 03 04improve- ment. Complete or nearly complete remission of all symptomsModerate Decided 05 06 07 08 improve- ment. Partial remission ofsymptoms Minimal Slight 09 10 11 12 improve- ment which doesn't alterstatus of care of patient Unchanged 13 14 15 16 or worse Not assessed 00Reproduced from Guy W, editor. ECDEU Assessment Manual forPsychopharmacology. 1976. Rockville, MD, U.S. Department of Health,Education, and Welfare

V. Treatment of Psychotic Disorders

As described herein, the presence of a SULT4A1-1 haplotype describedherein has been correlated with an altered response to a treatment,e.g., a pharmacological treatment. An altered response can be, forexample, a positive response (i.e., an improvement in one or moresymptoms of the disease), negative response (worsening of one or moresymptoms of the disease), no response, or the presence or absence ofside effects. Thus, the new methods can also include selecting ordeveloping a treatment regimen for a subject determined to or suspectedto have a psychotic disorder based upon the absence or presence of aSULT4A1-1 haplotype.

For example, the inventors identified a SULT4A1-1 haplotype anddeveloped its use in determining the optimal use of antipsychoticmedications: i) Patients who are SULT4A1-1 positive have a higherprobability of clinically significant improvement when treated witholanzapine when compared to patients who are SULT4A1-1 negative oruntested. ii) Patients who are SULT4A1-1 positive may have a higherprobability of clinically significant improvement when treated witholanzapine compared to other antipsychotic drugs. For example, thisSULT4A1-1 positive group responds better to olanzapine than torisperidone, quetiapine or perphenzazine. iii) Patients who areSULT4A1-1 negative have a lower probability of clinically significantimprovement when treated with olanzapine compared to similar patientswho are SULT4A1-1 positive. Since olanzapine has a significant metabolicside effect burden compared to alternative first-line antipsychoticsthat demonstrate non-inferiority to olanzapine, it may be appropriate torecommend that first-line antipsychotics with lower metabolicside-effect burdens than olanzapine be used preferentially for SULT4A1-1negative patients.

The methods can also include administering a selected treatment regimento a subject having, or suspected to have a psychotic disorder, tothereby treat, prevent or delay further progression of the disease. Atreatment regimen can include the administration of a selectedantipsychotic medications to a subject identified as at risk ofdeveloping a psychotic disorder, before the onset of any psychoticepisodes. The medications can be selected based on the status of aSULT4A1-1 haplotype that is associated with, for example, positiveresponse, or the absence of significant side effects.

As used herein, the term “treat” or “treatment” is defined as theprescription, application or administration of a treatment regimen,e.g., a therapeutic agent or modality, to a subject, e.g., a patient.The subject can be a patient having a symptom of a psychotic disorder,or at risk of developing (i.e., a predisposition toward) such adisorder. The treatment can be to cure, heal, alleviate, relieve, alter,remedy, ameliorate, palliate, improve or affect a psychotic disorder,the symptoms of a psychotic disorder, or the predisposition toward apsychotic disorder.

The methods described herein, e.g., methods of determining a treatmentregimen and methods of treatment or prevention of a psychotic disorder,can further include the step of monitoring the subject, e.g., for achange (e.g., an increase or decrease) in one or more of the diagnosticcriteria for a psychotic disorder, listed herein, or any other parameterrelated to clinical outcome. The subject can be monitored in one or moreof the following periods: prior to beginning of treatment; during thetreatment; or after one or more elements of the treatment have beenadministered. Monitoring can be used to evaluate the need for furthertreatment with the same or a different therapeutic agent or modality.Generally, a decrease in one or more of the parameters described aboveis indicative of the improved condition of the subject, although withred blood cell and platelet levels, an increase can be associated withthe improved condition of the subject.

For example, the methods can be used to evaluate the suitability of, orto choose between alternative treatments, e.g., a particular dosage,mode of delivery, time of delivery, inclusion of adjunctive therapy,administration in combination with a second agent, or generally todetermine the subject's probable drug response genotype. The effects ofthe treatment or combination of treatments on each of these subjects canbe used to determine if a treatment or combination of treatments isparticularly effective on a sub-group of subjects having a psychoticdisorder. In other embodiments, various treatments or combinations oftreatments can be evaluated by administering two different treatments orcombinations of treatments to at least two different subjects having apsychotic disorder, and a determined SULT4A1-1 haplotype status asdescribed herein. Such methods can be used to determine if a particulartreatment or combination of treatments is more effective than others intreating this subset of patients.

A. Risk of Discontinuation

As described herein, the presence or absence of the SULT4A1-1 haplotypedescribed herein has been correlated with the risk of discontinuation ofa particular treatment plan. A risk of discontinuation could be causedby factors such as a lack of efficacy or perceived lack of efficacy, orby treatment emergent side effects (TAEs). Thus, the new methods canalso include determining elevated risk of a patient to discontinuetreatment with a particular drug based upon the absence or presence of aSULT4A1-1 haplotype.

All of the drugs studied in CATIE have significant side-effect burdens.Thus, an important outcome measure was time to discontinuation for TAE.While the various TAEs are traditional safety measures that arereflected in the existing drug labels, segmentation by SULT4A1-1haplotype status produces special subpopulations for which the ratesand/or severity of the TAE are altered and for which new label languagemay be appropriate (e.g., as seen for the drug metabolism enzymes).Accordingly, segmentation by SULT4A1-1 status can lead to an alteredrisk/benefit profile.

For example, the inventors identified the SULT4A1-1 haplotype anddeveloped its use in determining the risk of discontinuation of anantipsychotic medication: i) Patients who are SULT4A1-1 negative have anelevated risk of discontinuation due to treatment-emergent adverseevents (TAEs) when treated with olanzapine. ii) Patients who areSULT4A1-1 positive have an elevated risk of discontinuation when treatedwith risperidone. iii) Patients who are SULT4A1-1 positive have anelevated risk of discontinuation as measured by all-causediscontinuation when treated with risperidone. iv) Patients who areSULT4A1-1 positive have an elevated risk of discontinuation due to lackof efficacy when treated with risperidone. v) Patients who are SULT4A1-1positive have elevated risk of discontinuation due to treatment emergentside effects when treated with risperidone.

The methods described herein, e.g., methods of determining elevated riskof a patient to discontinue treatment with a particular drug, mayinclude determining the propensity of a patient to continue ordiscontinue treatment based on the SULT1A1-1 haplotype. As used herein,“propensity to continue treatment” is defined as having a lower risk ofdiscontinuing treatment as defined by a Hazard Ratio of less than 1. TheHazard Ratio measures the risk of an event relative to exposure bycomparing the risk of an event in a target group to the risk of the sameevent in a control group. For example, a HR of 2 would mean that thosepatients in the target group are twice as likely to experience theevent, e.g., discontinue a treatment plan when compared to those in acontrol group, while a HR of 0.5 means that the patients in the targetgroups would have 50% lower risk of experiencing the event. As usedherein, “propensity to discontinue treatment” is defined as having anincreased risk of discontinuing treatment as defined by a Hazard Ratioof greater than 1.

The methods described herein may further comprise selecting apharmacotherapeutic treatment plan for a subject comprising determiningthe SULT4A1-1 haplotype and its relation to factors such as efficacy andthe risk of discontinuance for reasons such as treatment-emergentadverse events, selecting a pharmacotherapeutic treatment plan based onthe SULT4A1-1 haplotype, and treating the subject with the selectedpharmacotherapeutic treatment.

B. Current Treatments for Psychotic Disorders

Atypical antipsychotic drugs listed in order of current prescribingfrequency for these disorders include: risperidone, quetiapine,olanzapine, aripiprazole, ziprasidone, clozapine, paliperidone, andiloperidone. Typical antipsychotic drugs include haloperidol,fluphenazine, perphenazine, and others (Meltzer and Bobo, 2009).Atypical antipsychotics are favored because of lower parkinsonian sideeffects and perceived greater efficacy. There are several long actingformulations of typical antipsychotic drugs, which are seldom used inthe US. Among the atypical agents, only long acting, injectablerisperidone is currently available; long acting paliperidone palmitateis about to be approved, and others, e.g., long acting aripiprazole, arein development. These formulations are highly effective since theyprovide great help with regard to compliance, an enormous problem withboth bipolar and schizophrenia patients. However, they are underutilizedin the marketplace.

All of the antipsychotic medications have some degree of side-effectsand other limitations. Metabolic side effects with some atypicalantipsychotic drugs (weight gain, increased lipids, and problems withglucose regulation, including diabetes) exacerbate the discontinuationrates and limit overall effectiveness the implicated drugs. Olanzapineand clozapine, two of the most efficacious drugs for treating psychosis,have the greatest incidence of metabolic side-effects (Nasrallah, 2007).

Subjects with SZ typically require acute treatment for psychoticexacerbations, and long-term treatment including maintenance andprophylactic strategies to sustain symptom improvement and preventrecurrence of psychosis. Subjects with schizoaffective disorderexperience the symptoms of both SZ and affective disorder (manic and/ordepressive), thus require the specific treatments for each disorder.Subjects with SPD sometimes require medication for acute psychoticepisodes but are often treated using psychosocial methods. The methodsdescribed herein can include the administration of one or more acceptedor experimental treatment modalities to a person identified as having,suspected to have, or at risk of developing a psychotic disorder such asSZ, SPD, or a SD, based on the determination of a SULT4A1-1 haplotypestatus. Currently accepted treatments presently include bothpharmacologic and psychosocial management, and occasionallyelectroconvulsive therapy (ECT).

Standard pharmacologic therapies for SZ and SD include theadministration of one or more antipsychotic medications, which aretypically antagonists acting at postsynaptic D₂ dopamine receptors inthe brain. Antipsychotic medications include conventional, or firstgeneration, antipsychotic agents, which are sometimes referred to asneuroleptics because of their neurologic side effects, and secondgeneration antipsychotic agents, which are less likely to exhibitneuroleptic effects and have been termed atypical antipsychotics.

Anti-psychotic treatment for SD also include the administration of acombination of antidepressant, and anti-anxiety medication. Suitableantidepressants include serotonergic antidepressants, e.g., fluoxetineor trazodone. Suitable anxiolytics include benzodiazepines, e.g.,lorazepam, clonazepam. Lithium can also be administered. Thus, in someembodiments, the methods can include the administration of one or moreantidepressant and/or anti-anxiety medications to a person identified ashaving or suspected to have SD in combination with a treatment planbased on SULT4A1-1 haplotype status.

The methods can also include psychosocial and rehabilitationinterventions, e.g., interventions that are generally accepted astherapeutically beneficial, e.g., cognitive-behavioral therapy fortreatment-resistant positive psychotic symptoms; supportive,problem-solving, educationally oriented psychotherapy; family therapyand education programs aimed at helping patients and their familiesunderstand the patient's illness, reduce stress, and enhance copingcapabilities; social and living skills training; supported employmentprograms; and/or the provision of supervised residential livingarrangements.

Currently accepted treatments for SZ are described in greater detail inthe Practice Guideline for the Treatment of Patients With Schizophrenia,2004, which is incorporated herein by reference in its entirety.

Currently accepted treatments for BD are described in greater detail inthe Treatment of Patients With Bipolar Disorder, 2006, which isincorporated herein by reference in its entirety.

There are seven commonly prescribed atypical antipsychotic medicationsfor bipolar disorder:

Abilify (aripiprazole)

Risperdal (risperidone)

Zyprexa (olanzapine)

Seroquel (quetiapine)

Geodon (ziprasidone)

Cloazril (clozapine)

Symbyax (olanzapine/fluoxetine)

The atypical antipsychotics have several significant side-effects,including weight gain, metabolic and hormonal dysregulation, and sexualdysfunction. Weight gain, in particular, can be a significant issue asmany people treated with atypical antipsychotics expect to gain weight,sometimes significantly so. Because weight gain is also associated withan increased risk for Type II diabetes, individuals taking an atypticalantipsychotic should be carefully monitored by their physician. Othermetabolic disturbances include elevated prolactin levels and alteredsteroid metabolism. Additionally, both men and women report significantlevels of sexual dysfunction.

Drugs approved for the treatment of bipolar disorder can have one ormore indications, e.g., U.S. FDA (or other regulatory body) approveduses. Some of these indications include: Treatment of Acute Maniaepisodes; Bipolar Mania maintenance; Bipolar depression; Treatment ofmixed mania and depression episodes.

Clinicians most commonly initiate treatment with oral risperidone,especially now that it is generic. Often, however, clinicians willswitch patients to another drug after less than 1 to 6 months oftreatment. This common practice occurs based on what is perceived bypatients and clinicians as both insufficient efficacy and unacceptableside effects, such as Parkinsonism, prolactin elevations or weight gain.Olanzapine, which was found to be the most effective treatment in theCATIE study and is closest in pharmacology to clozapine (the druggenerally accepted to have the highest efficacy, particularly intreatment resistant subjects), is considered to be a highly effectiveagent (Meltzer and Bobo, 2009). Indeed, olanzapine became the mostprescribed treatment and initial drug of choice after its introductionuntil concerns about metabolic side effects became evident (Meltzer,2005). Metabolic side effects (weight gain, glucose dysregulation, lipiddysregulation and risk of diabetes) have greatly reduced the utilizationof olanzapine despite its high efficacy.

C. Pharmacogenetic Testing

Clinicians currently have no way of knowing which drug is best for aspecific patient other than from previous successful or unsuccessfultrials. They make decisions based on their overall experience with agiven drug as well as the influence of advertising and recommendationsfrom clinic supervisors. Also options may be limited because, without amedical rationale, many states limit access to highly efficaciousmedications (primarily olanzapine) for Medicaid recipients due to costconcerns.

Payers would welcome a diagnostic test that enhances compliance andresponse rates for their clients. Compliance with oral antipsychoticdrugs is a major problem, with 50% of patients ceasing to take themwithin 6 months of prescription, leading to relapse (return ofpsychosis) and hospitalization. While U.S. consumers and governmentagencies spend a considerable amount of money on atypical drugs, relapseand hospitalization represent the largest costs associated withschizophrenia and bipolar disorders. Thus, reducing the rate ofhospitalizations and relapse can lead to very significant cost savingsand improved patient care.

It is consensus opinion among experts in the treatment of schizophreniathat a pharmacogenetic test which could deliver information that led toa more rapid and extensive control of psychosis would become thedominant driver of choice of medication options. Physicians could engagepatients in a rational dialogue regarding treatment choice based ongenetic profile. With this additional information, physicians andpatients could make calculated risk-benefit analysis regarding potentialefficacy and side-effect concerns of the various antipsychoticmedications. There is also a published cost-effectiveness analysis whichsupports the value of pharmacogenetic testing (Perlis et al., 2005).

With regards to both prophylactic and therapeutic methods of treatmentof psychotic disorders, such treatments may be specifically tailored ormodified, based on knowledge obtained from the field ofpharmacogenomics. “Pharmacogenomics,” as used herein, refers to theapplication of genomics technologies such as structural chromosomalanalysis, to drugs in clinical development and on the market. See, forexample, Eichelbaum et al. (1996) and Linder et al. (1997).Specifically, as used herein, the term refers the study of how apatient's genes determine his or her response to a drug (e.g., apatient's “drug response phenotype,” or “drug response genotype”). Thus,another aspect of the invention provides methods for tailoring anindividual's prophylactic or therapeutic treatment according to thatindividual's drug response genotype, especially, a SULT4A1-1 haplotypestatus.

Information generated from pharmacogenomic research using a methoddescribed herein can be used to determine appropriate dosage andtreatment regimens for prophylactic or therapeutic treatment of anindividual. This knowledge, when applied to dosing or drug selection,can avoid adverse reactions or therapeutic failure and thus enhancetherapeutic or prophylactic efficiency when administering a therapeuticcomposition to a patient, as a means of treating or preventing psychoticdisorders.

In one embodiment, a physician or clinician may consider applyingknowledge obtained in relevant pharmacogenomics studies, e.g., using amethod described herein, when determining whether to administer apharmaceutical composition, e.g., an antipsychotic agent or acombination of antipsychotic agents, to a subject. In anotherembodiment, a physician or clinician may consider applying suchknowledge when determining the dosage, e.g., amount per treatment orfrequency of treatments, of a treatment, e.g., a antipsychotic agent orcombination of antipsychotic agents, administered to a patient.

As one example, information regarding a haplotype associated with analtered pharmacogenomic response for psychotic disorders as describedherein, can be used to stratify or select a subject population for aclinical trial. The information can, in some embodiments, be used tostratify individuals that may exhibit a toxic response to a treatmentfrom those that will not. In other cases, the information can be used toseparate those that are more likely to be non-responders from those whowill be responders. The SULT4A1-1 haplotypes described herein can beused in pharmacogenomics-based design and to manage the conduct of aclinical trial, e.g., as described in U.S. Pat. Pub. No. 2003/0108938.

As another example, information regarding a SULT4A1-1 haplotypeassociated with an increased severity of psychotic disorders, or withaltered pharmacogenomic response for psychotic disorders, as describedherein, can be used to stratify or select human cells or cell lines fordrug testing purposes. Human cells are useful for studying the effect ofa polymorphism on physiological function, and for identifying and/orevaluating potential therapeutic agents for the treatment of psychoticdisorders, e.g., anti-psychotics. Thus the methods can includeperforming the present methods on genetic material from a cell line. Theinformation can, in some embodiments, be used to separate cells thatrespond to particular drugs from those that do not respond to, e.g.which cells show altered second messenger signaling.

D. Theranostics

As used herein, the word “theranostic” is a combination of a specifictherapy and diagnostic. The combination represents the use of adiagnostic test to identify a specific patient subtype(s) of psychoticdisorders that have common genetic, clinical, metabolic, and/orprognostic features. By performing a diagnostic test, e.g. a genetictest to determine haplotypes for the SULT4A1 genes, the physician orclinician can place the patient into a specific disease sub-type orcategory, for example, a SULT4A1-1 positive or negative subgroup.Moreover, patients in such a sub-type respond to a given therapy in aparticular manner.

Also included herein are compositions and methods for the identificationand treatment of subjects who have an increased severity of a psychoticdisorder, or altered clinical presentation of a psychotic disorder, suchthat a theranostic approach can be taken to test such individuals todetermine the effectiveness of a particular therapeutic intervention(e.g., a pharmaceutical or non-pharmaceutical intervention as describedherein) and/or to alter the intervention to enhance the effectiveness.Thus, the methods and compositions described herein provide a means ofoptimizing the treatment of a subject having or suspected to have apsychotic disorder such as SZ. Provided herein is a theranostic approachto treating and preventing a psychotic disorder such as SZ, byintegrating diagnostics and therapeutics to improve the real-timetreatment of a subject. Practically, this means creating tests that canidentify which patients are most suited to a particular therapy, andproviding feedback on how well a drug is working to optimize treatmentregimens.

Within the clinical trial setting, a theranostic method or compositionof the invention can provide key information to optimize trial design,monitor efficacy, and enhance drug safety. For instance, “trial design”theranostics can be used for patient stratification, determination ofpatient eligibility (inclusion/exclusion), creation of homogeneoustreatment groups, and selection of patient samples that arerepresentative of the general population. Such theranostic tests cantherefore provide the means for patient efficacy enrichment, therebyminimizing the number of individuals needed for trial recruitment.“Efficacy” theranostics are useful for monitoring therapy and assessingefficacy criteria. Finally, “safety” theranostics can be used to preventadverse drug reactions or avoid medication error.

The methods described herein can include retrospective analysis ofclinical trial data as well, both at the subject level and for theentire trial, to detect correlations between a haplotype as describedherein and any measurable or quantifiable parameter relating to theoutcome of the treatment, e.g., efficacy (the results of which may bebinary (i.e., yes and no) as well as along a continuum), side-effectprofile (e.g., weight gain, metabolic dysfunction, lipid dysfunction,movement disorders, or extrapyramidal symptoms), treatment maintenanceand discontinuation rates, return to work status, hospitalizations,suicidality, total healthcare cost, social functioning scales, responseto non-pharmacological treatments, and/or dose response curves. Theresults of these correlations can then be used to influencedecision-making, e.g., regarding treatment or therapeutic strategies,provision of services, and/or payment. For example, a correlationbetween a positive outcome parameter (e.g., high efficacy, low sideeffect profile, high treatment maintenance/low discontinuation rates,good return to work status, low hospitalizations, low suicidality, lowtotal healthcare cost, high social function scale, favorable response tonon-pharmacological treatments, and/or acceptable dose response curves)and a SULT4A1-1 haplotype can influence treatment such that thetreatment is recommended or selected for a subject with the SULT4A1-1haplotype determined.

VI. Kits

Certain aspects of the present invention provide kits, such asdiagnostic and therapeutic kits. Kits may comprise a container with alabel. Suitable containers include, for example, bottles, vials, andtest tubes. The containers may be formed from a variety of materialssuch as glass or plastic. The container may hold a composition whichincludes a probe or an array that could be used to determine a SULT4A1-1haplotype, which could be effective for diagnostic or pharmacogenomicapplications. The label on the container may indicate that thecomposition is used for a specific diagnostic or pharmacogenomicapplication, and may also indicate directions for either in vivo or invitro use, such as those described above. The kit of the invention willtypically comprise the container described above and one or more othercontainers comprising materials desirable from a commercial and userstandpoint, including buffers, diluents, filters, needles, syringes, andpackage inserts with instructions for use.

Within the scope of the invention are kits comprising a probe thathybridizes with a region of human chromosome as described herein and canbe used to detect a polymorphism related to a SULT4A1-1 haplotype. Thekit can include one or more other elements including: instructions foruse; and other reagents, e.g., a label, or an agent useful for attachinga label to the probe. Instructions for use can include instructions fordiagnostic applications of the probe for assessing severity of apsychotic disorder such as SZ in a method described herein. Otherinstructions can include instructions for attaching a label to theprobe, instructions for performing in situ analysis with the probe,and/or instructions for obtaining a sample to be analyzed from asubject. As discussed above, the kit can include a label, e.g., any ofthe labels described herein. In some embodiments, the kit includes alabeled probe that hybridizes to a region of human chromosome asdescribed herein, e.g., a SULT4A1 polymorphic site as described herein.

The kit can also include one or more additional probes that hybridize tothe same chromosome, or another chromosome or portion thereof that canhave an abnormality associated with diagnostic applications. Forexample, the additional probe or probes can be: a probe that hybridizesto human chromosome 22q11-12 or a portion thereof, (e.g., a probe thatdetects a sequence associated with a psychotic disorder in this regionof chromosome 22), or probes that hybridize to all or a portion of22q12.3 (e.g., near D22S283), 22q11.2, 22q11.2, 22q11-q13, 1q42.1,1q42.1, 1q21-q22, 2p, 2q, 3p25, 4p, 4q, 5q11.2-q13.3, 6p22.3, 6p23,6q13-q26, 7q, 8p12-21, 8q, 9p, 10p15-p13 (e.g., near D10S189), 10q22.3,11q14-q21, 12q24, 13q34, 13q32, 14q32.3, 15q15, 16p, 17q, 18p, 18q, 19p.20p, 21q, Xq, and/or the X/Y pseudoautosomal region. A kit that includesadditional probes can further include labels, e.g., one or more of thesame or different labels for the probes. In other embodiments, theadditional probe or probes provided with the kit can be a labeled probeor probes. When the kit further includes one or more additional probe orprobes, the kit can further provide instructions for the use of theadditional probe or probes.

Kits for use in self-testing can also be provided. For example, suchtest kits can include devices and instructions that a subject can use toobtain a sample, e.g., of buccal cells or blood, without the aid of ahealth care provider. For example, buccal cells can be obtained using abuccal swab or brush, or using mouthwash.

Kits as provided herein can also include a mailer, e.g., a postage paidenvelope or mailing pack, that can be used to return the sample foranalysis, e.g., to a laboratory. The kit can include one or morecontainers for the sample, or the sample can be in a standard bloodcollection vial. The kit can also include one or more of an informedconsent form, a test requisition form, and instructions on how to usethe kit in a method described herein. Methods for using such kits arealso included herein. One or more of the forms, e.g., the testrequisition form, and the container holding the sample, can be coded,e.g., with a bar code, for identifying the subject who provided thesample.

Kits may also comprise or be coupled to a system which can makerecommendations and/or analysis of efficacy, risk or side effects fortreatment of a psychotic disorder based on a determined SULT4A1-1haplotype status. The system may comprise a server, a processor, or atangible computer readable program product. For example, if the kitdetermines the presence or absence of a SULT4A1-1 haplotype, the systemmay perform an analysis and generate an efficacy and/or risk profile fortreatment with a psychotic treatment, such as treating with olanzapine.

VII. Probes

Nucleic acid probes can be used to detect and/or quantify the presenceof a particular target nucleic acid sequence within a sample of nucleicacid sequences, e.g., as hybridization probes, or to amplify aparticular target sequence within a sample, e.g., as a primer. Probeshave a complimentary nucleic acid sequence that selectively hybridizesto the target nucleic acid sequence. In order for a probe to hybridizeto a target sequence, the hybridization probe must have sufficientidentity with the target sequence, i.e., at least 70%, e.g., 80%, 90%,95%, 98% or more identity to the target sequence, or any range derivabletherein. The probe sequence must also be sufficiently long so that theprobe exhibits selectivity for the target sequence over non-targetsequences. For example, the probe will be at least 10, e.g., 15, 20, 25,30, 35, 50, 100, 200, 300, 400, 500, 600, 700, 800, 900, or morenucleotides in length, or any range derivable therein. In someembodiments, the probes are not more than 30, 50, 100, 200, 300, 500,750, or 1000 nucleotides in length, or any range derivable therein.Specifically, probes may be about 20 to about 1×10⁶ nucleotides inlength. Probes include primers, which generally refers to asingle-stranded oligonucleotide probe that can act as a point ofinitiation of template-directed DNA synthesis using methods such as PCR(polymerase chain reaction), LCR (ligase chain reaction), etc., foramplification of a target sequence.

In some embodiments, the probe is a test probe, e.g., a probe that canbe used to detect polymorphisms in a region described herein, e.g.,SULT4A1 polymorphisms as described herein. In some embodiments, theprobe can hybridize to a target sequence within a region delimited bydelimiting SNPs, a first SNP (e.g., rs2285162 or rs2285166) and a secondSNP (e.g., rs2285167), for determination of a SULT4A1-1 haplotype.

In some embodiments, the probe can bind to another marker sequenceassociated with a psychotic disorder such as SZ as described herein.

Control probes can also be used. For example, a probe that binds a lessvariable sequence, e.g., repetitive DNA associated with a centromere ofa chromosome, can be used as a control. Probes that hybridize withvarious centromeric DNA and locus-specific DNA are availablecommercially, for example, from Vysis, Inc. (Downers Grove, Ill.),Molecular Probes, Inc. (Eugene, Oreg.), or from Cytocell (Oxfordshire,UK). Probe sets are available commercially, e.g., from AppliedBiosystems, e.g., the Assays-on-Demand SNP kits. Alternatively, probescan be synthesized, e.g., chemically or in vitro, or made fromchromosomal or genomic DNA through standard techniques. For example,sources of DNA that can be used include genomic DNA, cloned DNAsequences, somatic cell hybrids that contain one, or a part of one,human chromosome along with the normal chromosome complement of thehost, and chromosomes purified by flow cytometry or microdissection. Theregion of interest can be isolated through cloning, or by site-specificamplification via the polymerase chain reaction (PCR). See, for example,Nath and Johnson (1998); Wheeless et al. (1994); U.S. Pat. No.5,491,224.

In some embodiments, the probes are labeled, e.g., by direct labeling,with a fluorophore, an organic molecule that fluoresces after absorbinglight of lower wavelength/higher energy. A directly labeled fluorophoreallows the probe to be visualized without a secondary detectionmolecule. After covalently attaching a fluorophore to a nucleotide, thenucleotide can be directly incorporated into the probe with standardtechniques such as nick translation, random priming, and PCR labeling.Alternatively, deoxycytidine nucleotides within the probe can betransaminated with a linker. The fluorophore then is covalently attachedto the transaminated deoxycytidine nucleotides. See, e.g., U.S. Pat. No.5,491,224.

Fluorophores of different colors can be chosen such that each probe in aset can be distinctly visualized. For example, a combination of thefollowing fluorophores can be used: 7-amino-4-methylcoumarin-3-aceticacid (AMCA), Texas Red™ (Molecular Probes, Inc., Eugene, Oreg.),5-(and-6)-carboxy-X-rhodamine, lissamine rhodamine B,5-(and-6)-carboxyfluorescein, fluorescein-5-isothiocyanate (FITC),7-diethylaminocoumarin-3-carboxylic acid,tetramethylrhodamine-5-(and-6)-isothiocyanate,5-(and-6)-carboxytetramethylrhodamine, 7-hydroxycoumarin-3-carboxylicacid, 6-[fluorescein 5-(and-6)-carboxamido]hexanoic acid,N-(4,4-difluoro-5,7-dimethyl-4-bora-3a,4a diaza-3-indacenepropionicacid, eosin-5-isothiocyanate, erythrosin-5-isothiocyanate, and Cascade™blue acetylazide (Molecular Probes, Inc., Eugene, Oreg.). Fluorescentlylabeled probes can be viewed with a fluorescence microscope and anappropriate filter for each fluorophore, or by using dual or tripleband-pass filter sets to observe multiple fluorophores. See, forexample, U.S. Pat. No. 5,776,688. Alternatively, techniques such as flowcytometry can be used to examine the hybridization pattern of theprobes. Fluorescence-based arrays are also known in the art.

In other embodiments, the probes can be indirectly labeled with, e.g.,biotin or digoxygenin, or labeled with radioactive isotopes such as ³²Pand ³H. For example, a probe indirectly labeled with biotin can bedetected by avidin conjugated to a detectable marker. For example,avidin can be conjugated to an enzymatic marker such as alkalinephosphatase or horseradish peroxidase. Enzymatic markers can be detectedin standard colorimetric reactions using a substrate and/or a catalystfor the enzyme. Catalysts for alkaline phosphatase include5-bromo-4-chloro-3-indolylphosphate and nitro blue tetrazolium.Diaminobenzoate can be used as a catalyst for horseradish peroxidase.

Oligonucleotide probes that exhibit differential or selective binding topolymorphic sites may readily be designed by one of ordinary skill inthe art. For example, an oligonucleotide that is perfectly complementaryto a sequence that encompasses a polymorphic site (i.e., a sequence thatincludes the polymorphic site, within it or at one end), such asrs2285162, rs2285166, or rs2285167, will generally hybridizepreferentially to a nucleic acid comprising that sequence, as opposed toa nucleic acid comprising an alternate polymorphic variant.

VIII. Arrays and Uses Thereof

In another aspect, the invention features methods of determining theabsence or presence of a SULT4A1-1 haplotype using an array. In afurther aspect, the invention features arrays that include a substratehaving a plurality of addressable areas, and methods of using them. Atleast one area of the plurality includes a nucleic acid probe that bindsspecifically to a sequence comprising a polymorphism such as rs2285162,rs2285166, or rs2285167, and can be used to detect the absence orpresence of said polymorphism, e.g., one or more SNPs, microsatellites,minisatellites, or indels, to determine a SULT4A1-1 haplotype. Forexample, the array can include one or more nucleic acid probes that canbe used to detect a polymorphism such as rs2285162, rs2285166, orrs2285167. In some embodiments, the array further includes at least onearea that includes a nucleic acid probe that can be used to specificallydetect another marker associated with a psychotic disorder such as SZ asdescribed herein. The substrate can be, e.g., a two-dimensionalsubstrate known in the art such as a glass slide, a wafer (e.g., silicaor plastic), a mass spectroscopy plate, or a three-dimensional substratesuch as a gel pad. In some embodiments, the probes are nucleic acidcapture probes.

Methods for generating arrays are known in the art and include, e.g.,photolithographic methods (see, e.g., U.S. Pat. Nos. 5,143,854;5,510,270; and 5,527,681), mechanical methods (e.g., directed-flowmethods as described in U.S. Pat. No. 5,384,261), pin-based methods(e.g., as described in U.S. Pat. No. 5,288,514), and bead-basedtechniques (e.g., as described in PCT US/93/04145). The array typicallyincludes oligonucleotide probes capable of specifically hybridizing todifferent polymorphic variants. According to the method, a nucleic acidof interest, e.g., a nucleic acid encompassing a polymorphic site,(which is typically amplified) is hybridized with the array and scanned.Hybridization and scanning are generally carried out according tostandard methods. See, e.g., Published PCT Application Nos. WO 92/10092and WO 95/11995, and U.S. Pat. No. 5,424,186. After hybridization andwashing, the array is scanned to determine the position on the array towhich the nucleic acid hybridizes. The hybridization data obtained fromthe scan is typically in the form of fluorescence intensities as afunction of location on the array.

Arrays can include multiple detection blocks (i.e., multiple groups ofprobes designed for detection of particular polymorphisms). Such arrayscan be used to analyze multiple different polymorphisms. Detectionblocks may be grouped within a single array or in multiple, separatearrays so that varying conditions (e.g., conditions optimized forparticular polymorphisms) may be used during the hybridization. Forexample, it may be desirable to provide for the detection of thosepolymorphisms that fall within G-C rich stretches of a genomic sequence,separately from those falling in A-T rich segments.

Additional description of use of oligonucleotide arrays for detection ofpolymorphisms can be found, for example, in U.S. Pat. Nos. 5,858,659 and5,837,832. In addition to oligonucleotide arrays, cDNA arrays may beused similarly in certain embodiments of the invention.

The methods described herein can include providing an array as describedherein; contacting the array with a sample, e.g., a portion of genomicDNA that includes at least a portion of human chromosome 22, e.g., aregion between and/or including SNPs for a SULT4AJgene, and/oroptionally, a different portion of genomic DNA, e.g., a portion thatincludes a different portion of human chromosomes 1, 2, 3, 4, 5, 6, 7,8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 and/or 22, oranother chromosome, e.g., including another region associated with apsychotic disorder, pharmacological response, and/or psychiatricendophenotypes, and detecting binding of a nucleic acid from the sampleto the array. Optionally, the method includes amplifying nucleic acidfrom the sample, e.g., genomic DNA that includes a portion of a humanchromosome described herein, and, optionally, a region that includesanother region associated with a psychotic disorder, pharmacologicalresponse, and/or psychiatric endophenotypes, prior to or during contactwith the array.

In some aspects, the methods described herein can include using an arraythat can ascertain differential patterns of one or more genes in samplesfrom normal and affected individuals (see, e.g., Redon et al., 2006).For example, arrays of probes to a marker described herein can be usedto measure polymorphisms between DNA from a subject having a psychoticdisorder and control DNA, e.g., DNA obtained from an individual thatdoes not have a psychotic disorder and has no familial risk factors fora psychotic disorder. Since the clones or probes on the array containsequence tags, their positions on the array are accurately knownrelative to the genomic sequence. Different hybridization patternsbetween DNA from an individual afflicted with a psychotic disorder suchas SZ and DNA from a normal individual at areas in the arraycorresponding to markers in human chromosome 1, 2, 3, 4, 5, 6, 7, 8, 9,10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 and/or 22 as describedherein, and, optionally, one or more other regions associated with apsychotic disorder are indicative of a risk of SZ-spectrum disorders.Methods for array production, hybridization, and analysis are described,e.g., in Snijders et al. (2001); Klein et al. (1999); Albertson et al.(2003); and Snijders et al. (2002). Real time quantitative PCR can alsobe used to determine copy number differences.

IX. Examples

The following examples are included to demonstrate preferred embodimentsof the invention. It should be appreciated by those of skill in the artthat the techniques disclosed in the examples which follow representtechniques discovered by the inventor to function well in the practiceof the invention, and thus can be considered to constitute preferredmodes for its practice. However, those of skill in the art should, inlight of the present disclosure, appreciate that many changes can bemade in the specific embodiments which are disclosed and still obtain alike or similar result without departing from the spirit and scope ofthe invention.

Example 1 Characterization of the Haplotype Structure of the SULT4A1Gene

The CATIE study, a large federally funded clinical trial designed toassess the efficacy of antipsychotics in a real world setting, is avaluable resource for determining the role of genes in baselinepsychopathology and drug response (Lieberman et al., 2005; Stroup etal., 2003). As part of the CATIE trial, detailed clinical evaluationswere conducted, including Positive and Negative Syndrome Scale (PANSS)measurements at multiple time points, cognitive evaluation, vital signs,blood chemistry results, and drug response data. Additionally, wholegenome SNP genotyping was performed for roughly half of the trialparticipants (Sullivan et al., 2008).

The inventors used samples collected in the course of the CATIE trial tostudy SULT4A1 haplotypes to determine if one or more specific haplotypesmight contribute to the clinical differences in SSD patients. Theinventors contemplated that one or more commonly occurring haplotypesmight account for the role of the SULT4A1 gene in the clinicalpresentation of SSDs. A relatively simple pattern of haplotypes wasanticipated, because the gene is highly conserved between species (Liyouet al., 2003; Minchin et al., 2008) and is characterized by a low degreeof sequence variation in human populations, displaying a low level ofSNP variation even in the introns (Hildebrandt et al., 2007; Lewis andMinchin, 2009). Previous studies in independent sample sets implicatedallelic variation in the gene in the genetic etiology and degree ofpsychopathology of SSDs, but the role of specific haplotypes had notbeen evaluated previously (Brennan and Condra, 2005; Condra et al.,2007; Meltzer et al., 2008).

A. Data and Methods Relating to the CATIE Sample

Genotype and phenotype data for the CATIE trial were recently madeavailable to qualified researchers through the NIMH Center forCollaborative Genetic Studies on Mental Disorders. For the Caucasian(European American) sample, the inventors evaluated data for 417 CATIEschizophrenia patients, and 419 normal controls self reported as havingexclusively European ancestry. This same population was described in arecent study by Sullivan and coworkers, which confirmed that there is nohidden stratification in the sample (Sullivan et al., 2008). The AfricanAmerican sample comprised genotypes for 218 schizophrenia patients and224 normal controls provided by the CATIE study.

The CATIE genotype data included a total of 11 SNPs located between thepreviously evaluated rs138110, in the promoter region, and the terminalexon of the gene (Brennan and Condra, 2005; Condra et al., 2007; Meltzeret al., 2008). From lowest to highest base pair position on thechromosome the CATIE SNPs were rs138067 (the SNP is in position 31 ofSEQ ID NO:2), rs138079 (the SNP is in position 31 of SEQ ID NO:3),rs470089 (the SNP is in position 31 of SEQ ID NO:4), rs2285161 (the SNPis in position 31 of SEQ ID NO:5), rs2285162 (the SNP is in position 31of SEQ ID NO:6), rs2285164 (the SNP is in position 31 of SEQ ID NO:7),rs2285167 (the SNP is in position 31 of SEQ ID NO:9), rs470091 (the SNPis in position 31 of SEQ ID NO:10), rs138099 (the SNP is in position 31of SEQ ID NO:11), rs138102 (the SNP is in position 31 of SEQ ID NO:12),rs138110 (the SNP is in position 31 of SEQ ID NO:13).

B. Methods for Initial Haplotype Discovery and Characterization

The initial genetic analysis to determine the identity and frequency ofSULT4A1 haplotypes was performed using the publicly available Haploviewprogram (Barrett et al., 2005; Haploview, Broad Institute 2009). Thissoftware assigns expectation-maximization (EM) algorithm—basedhaplotypes to each individual.

To examine the relationship of haplotypes to psychopathology, baselinePANSS scores were analyzed as quantitative traits by linear regressionusing the publicly available PLINK software (Purcell et al., 2007;available via pngu.mgh.harvard.edu/˜purcell/plink/). For theschizophrenia patients in the CATIE study, the clinical data setincluded baseline PANSS scores that were based on clinical assessmentsprior to initiation of the assigned therapy but following the washoutperiod for any patients previously on antipsychotic medication.

C. SULT4A1 Haplotypes in Caucasians and African Americans

As shown in FIG. 1, the Caucasian population displays a high degree oflinkage disequilibrium for the region covered by the SNPs. Correlationcoefficients (r²) values for several pairs of SNPs exceed 95%.

In fact, E-M maximum likelihood phasing of the 11 SNPs indicated thatthese markers define only seven haplotypes with frequencies≧0.5% inCaucasians (Table 1). The haplotype designated SULT4A 1-1, occurs at afrequency of 12%.

TABLE 1  SULT4A1 Haplotypes in Caucasians Frequency Haplotype^(a)Designation  % ACGCAAGCTCA  SULT4A1-1 12.0 (SEQ ID NO: 16) ACGCCGGCTCA SULT4A1-2 13.6 (SEQ ID NO: 17) ACGCAAACTCA  SULT4A1-3 14.9(SEQ ID NO: 18) ATGCCGGCTCA  SULT4A1-4 15.4 (SEQ ID NO: 19) GCACCGGTCTG SULT4A1-5 20.9 (SEQ ID NO: 20) GCGTCGGCTCG  SULT4A1-6 21.9(SEQ ID NO: 21) GCACCAGTCTG  SULT4A1-7 0.6 (SEQ ID NO: 22)ALL OTHERS^(b) 0.7 ^(a)Haplotypes for the 11 CATIE SNPs were calculatedby EM algorithm maximization in Haploview. The marker order is rs138067,rs138079, rs470089, rs2285161, rs2285162, rs2285164, rs2285167,rs470091, rs138099, rs138102, rs138110. The rs2285162 and rs2285167SNPs, which could be used to determine SULT4A1-1 haplotype status, aredesignated by underlining. Note that the rs2285162 “A” allele occurs incombination with rs2285167 “G” only for the SULT4A1-1 haplotype.^(b)Four rare haplotypes were inferred: one appeared twice and threeappeared only once in the entire sample. All of these included theeither rs2285162(C) in combination with rs2285167(G) or rs2285162(A) incombination with rs2285167(A).

Table 1 allows one to draw an important conclusion relating to theSULT4A1-1 haplotype. Specifically, the extended, 11 SNP SULT4A1-1haplotype is uniquely tagged by the two-SNP combinationrs2285162(A)-rs2285167(G). Therefore, the rs2285162(A)-rs2285167(G)combination is both necessary and sufficient to identify the presence ofthe entire extended SULT4A1-1 haplotype.

As shown in FIG. 2, the African American population displays somewhatless linkage disequilibrium for the region. However, the pattern issimilar to what was observed in the Caucasian population.

For African Americans, E-M maximum likelihood phasing of the 11 SNPsindicated that these markers define nine extended haplotypes withfrequencies≧0.5% (Table 2). The SULT4A1-1 haplotype is rarer than in theCaucasian Sample occurring at a frequency of only 5.2% in AfricanAmericans compared to a frequency of 12% in Caucasians. Despite thisdifference in frequency, the rs2285162(A)-rs2285167(G) sub-haplotype isboth necessary and sufficient to identify the presence of the extendedSULT4A1-1 haplotype in African Americans.

TABLE 2 SULT4A1 Haplotypes in African Americans Frequency Haplotype^(a)Designation  % ACGCAAGCTCA SULT4A1-1 5.2 (SEQ ID NO: 16) ACGCCGGCTCA SULT4A1-2 37.1 (SEQ ID NO: 17) ACGCAAACTCA  SULT4A1-3 3.9(SEQ ID NO: 18) ATGCCGGCTCA  SULT4A1-4 6.4 (SEQ ID NO: 19) GCACCGGTCTG SULT4A1-5 29.4 (SEQ ID NO: 20) GCGTCGGCTCG  SULT4A1-6 9.0(SEQ ID NO: 21) GCACCAGTCTG  SULT4A1-7 0.2 (SEQ ID NO: 22) ACGCCGGCTCG SULT4A1-8 5.6 (SEQ ID NO: 23) GCGCCGGCTCA  SULT4A1-9 0.9 (SEQ ID NO: 24)GCGCCGGTCTG  SULT4A1-10 0.7 (SEQ ID NO: 25) ALL OTHERS^(b) 1.6^(a)Haplotypes for the 11 CATIE SNPs were calculated by EM algorithmmaximization in Haploview. The marker order is rs138067, rs138079,rs470089, rs2285161, rs2285162, rs2285164, rs2285167, rs470091,rs138099, rs138102, rs138110. The rs2285162 and rs2285167 SNPs, whichcould be used to determine SULT4A1-1 haplotype status, are designated byunderlining. Note that the rs2285162 “A” allele occurs in combinationwith rs2285167 “G” only for the SULT4A1-1 haplotype. ^(b)Nine additionalrare haplotypes were inferred. All of these included the rs2285162(C) incombination with rs2285167(G).

The greater diversity of Haplotypes in the African American sample isexpected based upon the well established greater genetic diversity ofAfrican Americans relative to European Americans. Nonetheless, as wasseen in the Caucasian sample, the rs2285162(A)-rs2285167(G) combinationis both necessary and sufficient to identify the presence of the 11 SNPSULT4A1-1 haplotype in African Americans.

To confirm these findings, the inventors used two additional approaches.The inventors evaluated linkage disequilibrium and pre-calculatedhaplotype data available from the International HapMap Project (2009)for Europeans (CEU population) and African Americans (ASW population).Additionally, the inventors performed EM algorithm analysis forgenotypes of approximately 2,600 Caucasian samples and 2,600 AfricanAmerican samples made available by the National Institutes of MentalHealth on behalf of the dbGAP consortium (2009).

In brief, these additional analyses confirm that thers2285162(A)-rs2285167(G) haplotype is sufficient to tag the SULT4A1-1haplotype in both Caucasians and African Americans for a regioncorresponding to that covered by the 11 CATIE SNPs. These analyses alsodemonstrate that the rs2285166 is in complete linkage disequilibriumwith rs2285162, such that the rs2285166(T)-rs2285167(G) haplotypesuffices to uniquely tags the SULT4A1-1 haplotype.

Furthermore, these analyses did highlight one important differencebetween the Caucasian and African American populations. In Caucasians,the SULT4A1-1 haplotype extends beyond the region covered by the 11CATIE SNPs, encompassing the promoter region and the 3′ terminal exon.For African Americans, however, this relationship holds for less thanhalf of the extended haplotypes tagged by the two-SNP core haplotypes.

Example 2 The SULT4A1-1 Haplotype Correlates with Psychopathology inCaucasians

Linear regression analysis using PLINK indicated that the SULT4A1-1haplotype showed a significant association with baseline PANSS scoresfor Caucasian schizophrenia patients in the CATIE study (Table 3;P=0.03). This haplotypes explains approximately 1% of the variance witha beta weight of 4.0, corresponding to an increase in total PANSS scoreof 4.0 associated with the haplotype.

TABLE 3 Correlation of SULT4A1 Haplotypes with PANSS Total Score in CATIE Haplotype (designation)^(a) FrequencyBeta^(b) P value^(c) ACGCAA[G]GCTCA 0.116 4.00 0.034 (SULT4A1-1)(SEQ ID NO: 26) ACGCCG[A]GCTCA 0.125 0.46 0.723 (SULT4A1-2)(SEQ ID NO: 27) ACGCAA[G]ACTCA 0.145 −0.05 0.753 (SULT4A1-3)(SEQ ID NO: 28) ATGCCG[A]GCTCA 0.158 −2.04 0.287 (SULT4A1-4)(SEQ ID NO: 29) GCACCG[G]GTCTG 0.222 −1.67 0.344 (SULT4A1-5)(SEQ ID NO: 30) GCGTCG[G]GCTCG 0.237 0.17 0.784 (SULT4A1-6)(SEQ ID NO: 31) ^(a)Haplotypes for the 11 CATIE SNPs were calculated byEM algorithm maximization in PLINK. The marker order is rs138067,rs138079,rs470089, rs2285161, rs2285162, rs2285164, rs2285167, rs470091,rs138099, rs138102, rs138110. SNP rs138110 was used in previous studiesand is designated by underlining. Alleles for a second SNP used inprevious studies (rs138097, square brackets) were inferred using datafrom the International HapMap project. ^(b)Beta weights (regressioncoefficients) for quantitative trait, general linear model in PLINK.^(c)Asymptotic P value for the t-statistic (N = 417; Caucasian only).

This relationship did not hold for the African American patients in theCATIE sample. This could reflect the smaller sample size for the AfricanAmerican samples or the fact that the 11 SNP SULT4A1-1 haplotype doesnot capture allelic variation over an extended region in AfricanAmericans.

To determine if the SULT4A1-1 haplotype affects baselinepsychopathology, individuals from the CATIE study were scored for thepresence of the SULT4A1-1 haplotype using the rs2285162(A)-rs2285167(G)core haplotype (See Example 3 for details), and total baseline PANSSscores for groups with and without the haplotype were compared. Table 4shows the baseline PANSS scores for the two haplotype groups in theCATIE sample. The frequency of SULT4A1-1 positive patients isapproximately 22-23% and does not differ from Hardy-Weinbergexpectations.

TABLE 4 Relationship of SULT4A1-1 Status to Baseline PANSS Score^(a)Sample SULT4A1-1 + SULT4A1-1 − CATIE 75.7 (18.0) N = 88 71.1 (17.2) N =307 ^(a)Total PANSS scores, means (standard deviation) for patientswhose SULT4A1-1 haplotype status could be assigned with errorprobabilities of <1%.

In summary, a two-SNP haplotype, rs2285162(A) [orrs2285166(T)]-rs2285167(G), is sufficient to tag an extended SULT4A1-1haplotype in Caucasians. This haplotype correlates with elevatedbaseline PANSS scores in Caucasian patients suffering from SSDs. Thefollowing example (Example 3) describes how SULT4A1-1 haplotype statuscan be inferred from genotype data, and Example 4 describespharmacogenetic findings relating to SULT4A1-1 haplotype test.

Example 3 Assigning SULT4A1-1 Haplotype Status

Finished genotypes provided by the NIMH Center for Collaborative GeneticStudies on Mental Disorders were used to establish SULT4A1-1 haplotypestatus using a simple and intuitive scoring method for the presence ofthis established haplotype. As described in the previous Examples, thers2285162(A) [or rs2285166(T)]-rs2285167(G) combination is bothnecessary and sufficient to identify SULT4A1-1 haplotype in Caucasians.

A. Genotyping Methodology

The inventors seek only to document the well established quality of thegenotyping methodologies used for the Examples, and do not mean to limitthe invention to the particular molecular platform. For example, theAffymetrix platform, a widely used commercially available platform, wasused in the CATIE study. The technology behind this platform has beenincluded in CLIA-approved genotyping tests at the manufactures' ownfacilities and at third party providers.

The data process by the inventors were derived from a large scalegenotyping project that used microarray-based whole genome SNPgenotyping approaches. The project was performed by the CATIE studygroup using Affymetrix and Perlegen microarray platforms (Sullivan etal., 2008).

The inventors were provided finished genotype data and do not haveaccess to raw data files such as .cel files. As described in theprevious and present examples, genotypes provided by others were used toestablish SULT4A1-1 haplotype status using a simple and intuitivescoring method for the presence of this established haplotype.

Details of the genotyping performed by the CATIE consortium, includingtheir rigorous quality control procedures, are described elsewhere(Sullivan et al., 2008). Briefly, peripheral venous blood was collected,and genomic DNA was extracted from lymphocytes. Analyses were performedat Perlegen Sciences in its CLIA, GLP facility using two microarraygenotyping systems. The first was the Affymetrix 500K “A” chipset (Nsp Iand Sty I chips, Santa Clara, Calif.) used as specified by themanufacturer. Detailed description of the SNP detection methodology canbe found in Affymetrix product documentation (world wide web viaaffymetrix.com/products_services/arrays/specific/500k.affx). Secondly,Perlegen used a custom 164K chip. The genotype calling methodology andextensive quality control measures used by the CATIE study group werereported by Sullivan and coworkers (Sullivan et al., 2008) and furtherdescribed in detail in the supplemental technical material provided bythe CATIE consortium (Sullivan et al., 2008, Supplementary Information).

As an example of the level of quality control used, the CATIE groupperformed duplicate analysis on 36 samples. The proportion of SNPs withnon-missing genotype calls that disagreed in these duplicated sampleswas 0.00291. As an additional control, 277 individuals were genotyped ata second facility using a different SNP-calling algorithm to investigatepotential site bias. Only 0.73% of called genotypes differed between thetwo sites.

B. Core SULT4A1-1 Haplotypes

Table 5 summarizes the observed frequencies for core haplotypesemploying the SNPs rs2285162, rs2285166 and rs2285167 in Caucasians. Theresults in Table 5 are based on E-M algorithm maximization estimates forapproximately 2,600 samples (see Example 1). Only three of the eighttheoretically possible haplotypes were observed.

TABLE 5 Core SULT4A1-1 Haplotypes in Caucasians Core Tagged ExtendedApproximate Haplotypes^(a) Haplotypes Frequency % ATG SULT4A1-1 12.0 CCGSULT4A1-2,-4,-5,-6,-7 73^(b) ATA SULT4A1-3 15.0^(c) ^(a)The marker orderis rs2285162, rs2285166, rs2285167. ^(b)Includes three rare extendedhaplotypes containing the CCG core haplotype. ^(c)Includes one rareextended haplotype containing the ATA core haplotype.

Table 6 summarizes the observed frequencies for core haplotypesemploying the SNPs rs2285162, rs2285166 and rs2285167 in AfricanAmericans. Again, these results are based on E-M algorithm maximizationestimates for approximately 2,600 samples (see Example 1). Only three ofthe eight theoretically possible haplotypes were observed.

TABLE 6 Core SULT4A1 Haplotypes in African Americans ApproximateHaplotypes^(a) Designation Frequency % ATG SULT4A1-1 5.2 CCGSULT4A1-2,4,5,6,7,8,9,10 90.9^(b) ATA SULT4A1-3 3.9 ^(a)The marker orderis rs2285162, rs2285166, rs2285167. ^(b)Includes all observed rarehaplotypes.

C. Using SNP Genotypes to Determine SULT4A1-1 Haplotype Status

For the SNPS available in the CATIE study, SULT4A1-1 status isdetermined based on the genotype of the SNPs, rs2285162(A or C inposition 31 of SEQ ID NO:6) and rs2285167(A or G in position 31 of SEQID NO:9). As described immediately above, these SNPs define only threecommon haplotypes. Accordingly, patients are designated as SULT4A1-1positive using the simple scoring method illustrated in Table 7.

TABLE 7 Assignment of SULT4A1-1 Haplotype Status in the CATIE Possiblehaplotype SULT4A1-1 rs2285162 rs2285167 combination status A/C G/G AG/CGPositive A/A A/G AG/AA Positive A/A G/G AG/AG Positive C/C G/G CG/CGNegative A/A A/A AA/AA Negative A/C A/G AA/CG Negative

The haplotype scoring can be automated in Microsoft Excel by combining aseries of logical arguments. For purposes of illustration, samples ofthe scoring by the Excel spreadsheet are reproduced below (Table 8).

TABLE 8 Sample output for SULT4A1-1 status calling by the ExcelSpreadsheet A F Sam- D E Positive G ple B C Call- Geno- status callSULT4A1-1 ID rs2285162 rs2285167 able? type possible? Status 1 A_C G_GYES A_C 1 1 G_G 2 A_A A_G YES A_A 1 1 A_G 3 A_A G_G YES A_A 1 1 G_G 4C_C G_G YES C_C 0 0 G_G 5 A_A A_A YES A_A 0 0 A_A 6 A_C A_G YES A_C 0 0A_G 7 ? G_G NO 0 8 C_C ? NO 0 9 ? G_G NO 0 10 ? ? NO 0

The example of Table 8 shown is for the rs2285162-rs2285167 combination.A similar scoring method is used for the rs2285166-rs2285167combination, by substituting the appropriate alleles of rs2285166 (theSNP is in position 31 of SEQ ID NO:14) for the corresponding alleles ofrs2285162 (the SNP is position 31 of SEQ ID NO:6). Failed genotypes,which are rare, are coded as question marks and result in “NO”designation in column “D”. Column “G” provides the haplotype status asfollows: 1=positive, 0=negative, and a blank cell indicates genotypingfailure requiring retesting.

In summary, SULT4A1-1 haplotype status can be assigned using a simpleand intuitive scoring method. This method is easily automated usinglogical functions in programs such as Microsoft Excel.

Example 4 Clinical Performance of SULT4A1-1 Haplotype

There are several different metrics for quantifying response in clinicaltrials of antipsychotic medications. The most commonly used psychometricinstrument is the Positive and Negative Syndrome Scale (PANSS), a30-item semi-quantitative instrument scored by clinical professionals(Kay et al., 1987). The greater the decrease in PANSS score, the betterthe clinical response. The most direct measure of clinical response isabsolute change in PANSS score. In addition to absolute change, theimprovement is often reported as a percentage change from baseline PANSSscore.

This percentage change in PANSS may be used to derive a categoricaldefinition of response, wherein subjects who meet a certain criticalthreshold of change are classified as responders and those that do notmeet that criterion are classified as non-responders. A decrease of atleast 20% in total PANSS is one commonly used threshold for response(Leucht et al., 2009).

Alternatively, many drug trials for antipsychotic medications reportresponse as quantitative changes in PANSS score (Leucht et al., 2009).This approach is particularly useful for trials with active comparatorsor in cases where claims of drug superiority or non-inferiority areimportant (i.e. where relative improvement in symptoms is a key factor).

Both approaches shed light on the clinical utility of the SULT4A1-1haplotype as a biomarker, so the inventors presented results for bothcategorical definitions of response and for quantitative changes inpercent PANSS.

A. Responder/Nonresponder Statistics Based on Haplotype Status

The design of the CATIE study has been described in detail by others(Lieberman et al., 2005; Stroup et al., 2003). Briefly, 1460 subjectswere randomly assigned one of several antipsychotics and those who didnot respond or who chose to quit their current medication werere-randomized to another drug. A total of 738 subjects consented toprovide DNA for genetic study. Details regarding SNP genotyping andquality control have been recently published (Sullivan et al., 2008).Retrospective genetic analyses, judged to be exempt from human studiesrequirements by an IRB, were conducted in the current study.

All tested patients were studied using well established clinicalendpoints comparing baseline, intermediate, and last observation carriedforward (LOCF) for the PANSS scores using CATIE data. LOCF analysis is acommonly used clinical endpoint for clinical trials for neuropsychiatricdrugs, with changes in PANSS scores of between negative 20% and negative30% used as typical endpoints to indicate clinically significantresponse (Leucht et al., 2009). To remove time on drug as a variable forthe CATIE trial, analysis was limited to only those patients who wererandomized to a different drug following the initial washout period(drug switchers).

As summarized in Table 9, when patients are segmented by SULT4A1-1status and treatment arm, olanzapine-treated SULT4A1-1 positive(Caucasian) subjects demonstrated a greater likelihood of achieving the20% PANSS decrease than any other group in CATIE. Several points may bemade regarding these data.

TABLE 9 Relationship of SULT4A1-1 Status to Drug Response in CATIECaucasians SULT4A1-1 Positive^(a) SULT4A1-1 Negative^(a) Drug ≦−20%≧−20% Responders ≦−20% ≧−20% Responders P-value^(b) Olanzapine 10 566.6% 10 33 23.2% 0.006 Risperidone 3 14 17.6%* 18 43 29.5%* 0.53Quetiapine 7 11 38.8% 13 50 20.6%** 0.12 Perphenazine 5 9 35.7% 16 4725.4%** 0.51 Ziprasidone 3 7 30.0% 6 32 15.7%** 0.37 All Drugs 28 4637.8% 63 205 23.5%** 0.02 All Except 18 43 29.5%* 53 172 23.6%** 0.40Olanzapine ^(a)Numbers of individuals showing the specified percentchange in total PANSS (LOCF). A greater response corresponds to a morenegative change in PANSS score, with individuals showing a change inPANSS of ≦−20% being categorized as responders. ^(b)χ² (Yates Corrected)based p-value comparing SULT4A1-1 positive subjects to SULT4A1-1negative subjects for the particular drug or combination of drugs.*Olanzapine-treated SULT4A1-1 positive subjects responded significantlybetter p < 0.05 **Olanzapine-treated SULT4A1-1 positive subjectsresponded significantly better p < 0.01

First, SULT4A1-1 positive patients have a statistically higherprobability of experiencing a clinical response using olanzapine therapywhen compared to patients who are SULT4A1-1 negative (P=0.006).Furthermore, this higher probability of response remains statisticallysignificant when comparing use of the drug in SULT4A1-1 positivepatients (10 out of 15 responded) to patients unselected for SULT4A1-1status (20 out of 58; P=0.05). Although when all drugs are consideredtogether, SULT4A1-1 positive patients do respond better than SULT4A1-1negative patients, statistically significant superiority is lost ifolanzapine-treated patients are omitted (Table 9, last two rows).

Second, SULT4A1-1 positive patients have a higher probability ofexperiencing a clinically significant response using olanzapine whencompared to other antipsychotic drugs. For olanzapine compared torisperidone, the difference is statistically significant (P=0.014).SULT4A1-1 positive patients also respond significantly better toolanzapine than to all other drugs considered together (P=0.018).

Third, SULT4A1-1 negative patients respond at similar rates to allmedications (with the possible exception of ziprasidone), but have alower probability of clinically significant response for olanzapinecompared to SULT4A1-1 positive patients. Therefore, SULT4A1-1 positivepatients appear to be a subset of patients who are particularly goodcandidates for olanzapine treatment, while there appears to be noefficacy advantage for olanzapine in SULT4A1-1 negative patients

The inventors also examined the impact of the SULT4A1-1 status on drugresponse in the African American patients from the CATIE trial (Table10). For self-described African Americans segmented using the two-SNPSULT4A1-1 haplotype test, the relative effectiveness of the drugs in thehaplotype groups did not resemble that observed for patients of Europeandescent. The SULT4A1-1 haplotype is relatively rare in AfricanAmericans, and the numbers are too small for valid statisticalevaluation. Furthermore, as discussed in Example 3, the core haplotypedoes not reproducibly tag an extended haplotype in African Americans.Accordingly, it is impossible to determine if the apparent responsedifferences are the result of random variation due to the small samplesizes of the SULT4A1-1 positive African American patients, reflectdifferences in the extended tagged haplotypes in African Americans, orresult from some other interacting system that differs between Africanand European Americans. Therefore, all further analyses focusedexclusively on Caucasian subjects.

TABLE 10 Relationship of SULT4A1-1 Status to Drug Response in CATIEAfrican Americans SULT4A1-1 Positive^(a) SULT4A1-1 Negative^(a) Re- Res-Drug ≦−20% ≧−20% sponders ≦−20% ≧−20% ponders Olanzapine 1 3   25% 15 3033.3% Risperidone 3 2   60% 7 34 17.1% Quetiapine 2 4 33.3% 9 25 26.5%Perphenazine 0 2   0% 10 27 27.0% Ziprasidone 0 3   0% 4 22 15.4% AllDrugs 6 14 30.0% 45 138 24.6% All Except 5 11 31.3% 30 108 21.7%Olanzapine ^(a)Numbers of individuals showing the specified percentchange in total PANSS (LOCF). A greater response corresponds to a morenegative change in PANSS score, with individuals showing a change inPANSS of ≦−20% being categorized as responders.

The inventors also examined the possibility of using different responsethresholds in CATIE. FIGS. 3 and 4 show the distribution of SULT4A1-1positive and negative subjects, respectively, that met three differentresponse thresholds for the various drugs. As can be seen, the resultsfor the 10% and 30% thresholds are qualitatively similar to those forthe 20% threshold. However, more stringent thresholds tend to amplifythe difference between SULT4A1-1 positive patients treated witholanzapine and the other groups. For example, at the 30% level,SULT4A1-1 positive subjects were about four times more likely to respondto olanzapine than to any other atypical drug (quetiapine, risperidone,or zipraside). Similarly, at the 30% threshold, response for this groupwas at least twice that of the SULT4A1-1 negative patients treated withany of the drugs.

In summary, the results for the CATIE study show olanzapine-treatedSULT4A1-1 positive subjects demonstrated the greater response than anyother group using a 20% threshold. While a more stringent thresholdcould have been used, the 20% level provides both a clinicallymeaningful difference in response and good discrimination betweenSULT4A1-1 positive and negative patients.

To summarize the results, using the 20% threshold, olanzapine-treatedSULT4A1-1 positive subjects demonstrated the highest levels of response.More stringent thresholds amplify the difference between this group andthe other haplotype/treatment combinations. However, the 20% levelprovided both a clinically meaningful difference in response and gooddiscrimination between SULT4A1-1 positive and negative patients.

B. Quantitative Response Based on Haplotype Status

As mentioned previously, the mean change in absolute or percent PANSSprovides an important measure of efficacy in patients undergoingantipsychotic treatments. Indeed, many pivotal trials in the psychosisfield used absolute and/or percentage change in PANSS Score as theprimary endpoint (Leucht et al., 2009). The performance of theinvestigational drug is then compared with placebo and/or an activecomparator. Therefore, in addition to examining a categorical definitionof clinically significant response, the inventors determined the impactof segmentation by SULT4A1-1 status on the quantitative measure ofclinical improvement—delta PANSS. For the purposes of illustration, theinventors have elected to use percent change rather than absolute changeso that the values seen herein are directly comparable to thedichotomous analysis shown above. The same analyses using the absolutechange produce essentially the same results.

Table 11 shows the mean and standard deviation for the percent change inresponse for each of the drug arms segmented by SULT4A1-1 status for theCATIE study. As can be seen from the table, the olanzapine-treatedSULT4A1-1 positive group displayed superiority to all other groups withat least a trend suggesting potential significance if replicated in alarger data set. Additionally, as seen with the categoricalresponder/non-responder definition, all drug arms except risperidonedemonstrated a numerically superior response for SULT4A1-1 positivepatients.

TABLE 11 Change in PANSS Values for the CATIE Study SULT4A1-1 PositiveSULT4A1-1 Negative DELTA DELTA Drug N PANSS %^(a) SD^(b) N PANSS %^(a)SD^(b) Olanzapine 15 −24 16 43 −3*** 22 Perphenazine 14 −10* 24 63 −3***25 Quetiapine 18  −9** 21 63  0*** 26 Risperidone 17  −5*** 21 61 −5***25 Ziprasidone 10  −8* 24 38 −4*** 18 All Drugs 74 −11** 22 268 −3*** 24All Drugs - Olz 59  −8*** 22 225 −3*** 24 ^(a)Mean change in PANSS scorefrom baseline to LOCF ^(b)Standard deviation of the mean *P < 0.1, **P <0.05, and ***P < 0.01 olanzapine-treated SULT4A1-1 positive respondedsignificantly better

Olanzapine overall efficacy advantage in CATIE can be explainedprimarily by the response of the SULT4A1-1 positive patients. Overallolanzapine shows superior response compared to the other drugs (deltaPANSS −9 vs. −4). For SULT4A1-1 positive patients, which account foronly 25.8% of the olanzapine arm, olanzapine shows superior response toall other drugs (delta PANSS −24 versus −8). However, for SULT4A1-1negative patients, olanzapine does not display superiority over theother drugs (−delta PANSS −3 versus −3).

Another way to consider the response of the various groups is to analyzethe difference in the mean PANSS changes. Table 12 compares variousdrug-SULT4A1-1 groups to olanzapine-treated SULT4A1-1 positive subjects.A negative mean difference between the groups indicates greater responsefor the olanzapine-treated SULT4A1-1 positive patients. Additionally,the effect size (mean difference/standard deviation of pooled sample) isincluded in this table. The importance of the effect size will bediscussed in Example 5. For now, however, take note that the effectsizes are greater than 0.5 suggesting the biomarker is identifyingimportant differences in treatment response.

TABLE 12 Relative Response of Olanzapine-Treated SULT4A1-1 PositiveSubjects Compared to Other Groups in CATIE Comparison - Olanzapine Meandifference^(a) Effect P- SULT4A1-1 + (95% CI) size^(b) Value^(c) Vsrisperidone SULT4A1-1 + −20.9 (−33.2 to −6.0) 0.93 0.006 Vs perphenazineSULT4A1-1 + −14.2 (−29.8 to 1.4) 0.68 0.07  Vs quetiapine SULT4A1-1 +−14.9 (−28.3 to −1.5) 0.75 0.03  Vs ziprasidone SULT4A1-1 + −16.1 (−32.7to 0.5) 0.77 0.06  Vs unsegmented SULT4A1-1 + −13.0 (−24.7 to −1.2) 0.600.03  Vs SULT4A1-1 + except olanzapine −16.3 (−28.2 to −4.3) 0.68 0.008Vs olanzapine SULT4A1-1 − −20.9 (−33.4 to −8.4) 0.93 0.001 Vsunsegmented olanzapine −15.5 (−27.8 to −3.2) 0.69 0.01  Vs unsegmented(all drugs) −19.6 (−31.7 to −7.5) 0.83 0.002 ^(a)Mean difference wascalculated by subtracting the mean delta PANSS of the comparator groupfrom the mean DELTA PANSS of the olanzapine-treated SULT4A1-1 +group^(b)Effect size was calculated by dividing the mean difference by thestandard deviation ^(c)P-value was calculated using the T-test forcomparison of 2 means

C. Time to Discontinuation Statistics Based on Haplotype Status

The primary endpoint for the CATIE study was time to discontinuation forall causes (Lieberman et al., 2005). Thus the inventors evaluated theeffect of SULT41-1 status on this important parameter. Olanzapine wasthe superior drug for this endpoint for the sample as a whole (Liebermanet al., 2005).

As shown in Table 13, however, after segmentation by haplotype status,the superiority of olanzapine for time to discontinuation is explainedlargely by the SULT4A1-1 positive patients. Olanzapine-treated SULT4A1-1negative patients did not display a statistically significant longertime to discontinuation compared to the same patient group treated withany other drug. Notably, the olanzapine-treated SULT4A1-1 positivesubjects had a numerically superior time to discontinuation compared anyother group. This difference is significant compared to all of theSULT4A1-1 negative groups with the exception of patients treated withrisperidone. The time to discontinuation for SULT4A1-1 positive patientstreated olanzapine was also significantly longer than for SULT4A1-1positive patients treated with perphenazine, risperidone, or all drugscombined.

TABLE 13 Time to Discontinuation in the CATIE Study SULT4A1-1 SULT4A1-1Positive Negative Drug N Months^(a) SD^(b) N Months^(a) SD^(b)Olanzapine 15 14.3 6.4 43 10.0** 7.3 Perphenazine 14 7.6** 7.4 63 10.6*7.4 Quetiapine 18 10.3 7.5 63 8.6*** 7.0 Risperidone 17 8.0*** 6.0 6111.3 7.2 Ziprasidone 10 11.7 7.0 38 8.2*** 6.9 All drugs 74 10.2** 7.1268 9.9** 7.2 All drugs except Olanzapine 59 9.2** 7.4 225 9.7** 7.2^(a)Mean time in months ^(b)Standard deviation of the mean *P < 0.1, **P< 0.05, and ***P < 0.01 olanzapine-treated SULT4A1-1 positive respondedsignificantly better; P-value calculated using the T-test for comparisonof 2 means

FIGS. 5 and 6 show the percentage of SULT4A1-1 positive and negativepatients, respectively, remaining on the various drugs throughout PhaseI of the CATIE study. Note that SULT4A1-1 positive patients tend to stayon olanzapine treatment longer compared to other drugs (FIG. 5). Incontrast, this relationship does not hold for SULT4A1-1 negativepatients (FIG. 6).

In conclusion, the SULT4A1-1 haplotype identifies a sub-population,SULT4A1-1 positive patients, having superior response to olanzapinecompared to SULT4A1-1 negative patients. Additionally, SULT4A1-1positive patients respond better to olanzapine than to otherantipsychotic drugs. Finally, for SULT4A1-1 negative patients,olanzapine does not demonstrate superiority to other medications. Asdiscussed in Example 5, the superiority of olanzapine for SULT4A1-1patients exceeds the superiority reported for this drug in a number ofkey clinical trials. SULT4A1-1 is thus an important biomarker thatdiscriminates between patient subsets who are more or less likely torespond to olanzapine. Testing for this biomarker has the potential toimprove treatment decision making in patients who are candidates forantipsychotic drug therapy.

Example 5 Clinical Utility of the Biomarker

The primary rationale for determining the SULT4A1-1 status of a patientis to alter medical practice in some manner. Currently in thepsychiatric space, physicians lack useful tools to help them select themost efficacious antipsychotic medication for individual patients. Allof the currently approved antipsychotics demonstrated superiority toplacebo for treating psychotic symptoms as part of their approvalprocess at the FDA. Examples of comparative effectiveness can be foundin any New Drug Approval, e.g. the olanzapine approval package (Zyprexa(olanzapine) Approval Package NDA 20-592. FDA, Center for DrugEvaluation and Research 1996 (Available from: world wide web viaaccessdata.fda.gov/drugsatfda_docs/nda/96/020592_Original ApprovalPkg%20.pdf)). However, a recently published meta-analysis ofregistration quality clinical trials showed only modest improvementsover placebo.

Table 14 shows the results for the atypical antipsychotics used in theCATIE study. The effect size is defined as the difference in the meanresponse for each drug minus the change in the placebo arm, divided bythe standard deviation. In this case, a negative number means a greaterimprovement in psychopathology, i.e. a greater reduction in PANSS.

Relative to placebo, these drugs had effect sizes ranging from −0.42 to−0.59. For comparison, the same metrics are provided forolanzapine-treated SULT4A1-1 positive patients compared to various otherSULT4A1-1-drug combinations from the CATIE study. The effect sizes ofthe latter ranged from −0.91 to −0.47. To place this in context, theeffect size for olanzapine-treated SULT4A1-1 positive vs. SULT4A1-1negative patients in CATIE was roughly 50% larger (−0.91 vs.-0.59) thanthe effect size seen when comparing olanzapine to placebo for apopulation not segment by SULT4A1-1 status.

TABLE 14 Effect Sizes of Atypical Antipsychotics Number Effect EffectEffect Size attributable of Size vs. Size to SULT4A1−1 status DrugStudies Placebo^(c) vs. FGA^(d) in CATIE Olanzapine 6 −0.59 −0.21−0.93^(a) Quetiapine 5 −0.42 0.01 −0.75^(b) Risperidone 7 −0.59 −0.25−0.93^(b) Ziprasidone 4 −0.48 −0.04 −0.77^(b) ^(a)Olanzapine-treatedSULT4A1-1 positive versus olanzapine-treated SULT4A1-1 negative^(b)Olanzapine-treated SULT4A1-1 positive versus “drug”-treatedSULT4A1-1 positive ^(c)Leucht et al. (2009) ^(d)FGA = first generationantipsychotics. Results from Davis et al. (2003).

Currently, clinical practice emphasizes the increased efficacy ofatypical antipsychotics over typical antipsychotics. The meta-analysisperformed by Davis et al. (2003) examined the efficacy advantage ofatypical antipsychotics compared to first generation, or typical,antipsychotics. This analysis revealed a very minor advantage for someof the atypical antipsychotics over typical antipsychotics with effectsizes ranging from −0.25 to 0.01. Only olanzapine and risperidone showeda significant advantage over typical antipsychotics. The effect sizesobserved for olanzapine treatment of SULT4A1-1 positive subjectscompared to olanzapine treatment of SULT4A1-1 negative patients or othertreatment of SULT4A1-1 positive subjects with other drugs is roughlyfour times that seen when comparing olanzapine or risperidone to firstgeneration antipsychotics.

Therefore, a pharmacogenetic test for SULT4A1-1 haplotype status willoffer physicians a tool to identify a sub-population for which there isa treatment option providing more than twice the efficacy advantage thatatypical antipsychotics offer relative to typical antipsychotics.

Another recent meta-analysis compared the effectiveness of the variousatypical antipsychotics to each other by using the weighted meandifference in raw PANSS scores. Olanzapine consistently showed modestsuperiority to quetiapine, risperidone, and Ziprasidone, as shown inTable 15. However, this modest increase in efficacy in unsegmentedpopulations is much smaller than the efficacy improvement observed forthe olanzapine-treated SULT4A1-1 positive subjects in the CATIE sample.For example, for SULT4A1-1 positive subjects in CATIE, compared torisperidone, olanzapine demonstrated almost five-times improvement thanlower bound of the 95% confidence interval of the meta-analysiscomparing the two drugs for unsegmented populations.

In conclusion, segmentation by SULT4A1-1 status identifies asub-population, SULT4A1-1 positive patients, that demonstrates superiorresponse to olanzapine. Moreover, this superiority exceeds thesuperiority demonstrated by olanzapine over placebo for unsegmentedpopulations. Conversely, SULT4A1-1 negative patients respond more poorlyto olanzapine than do SULT4A1-1 positive subjects. Finally, for theSULT4A1-1 negative patients, olanzapine does not demonstrate superiorityover other medications seen in the meta-analysis for patient populationsnot segmented by SULT4A1-1 status.

TABLE 15 Mean Difference in Total PANSS Score Between Olanzapine andOther Atypical Antipsychotics CATIE Meta- unsege- CATIE CATIE Olanzapinevs. analysis^(a) mented SULT4A1-1 + SULT4A1-1 − Risperidone −1.9 −3.5−16  0.5 (−3.3 to −0.6) Quetiapine −3.7 −6.2 −12.9 −3.8 (−5.4 to −1.9)Ziprasidone −8.3 −4.9 −17.9 −2.1 (−11.0 to −5.6) ^(a)Mean (95% CI) seeLeucht et al. (2009).

Example 6 Diagnostic Performance Using Categorical Definitions ofResponse

Several different measures of diagnostic performance can be used forcomparing dichotomous outcomes. Two important metrics include percentpositive agreement (PPA), a substitute for sensitivity and percentnegative agreement (PNA), a substitute for specificity. Table 16 belowpresents these measures of diagnostic performance at the 20% decrease intotal PANSS threshold in CATIE for olanzapine treatment of SULT4A1-1positive patients compared to other groups.

TABLE 16 Diagnostic Performance of the SULT4A1-1 Haplotype Test in theCATIE Study Using a 20% decrease in PANSS Threshold Non Compari- Res-Res- PPA^(b) PNA^(c) DOR^(d) son^(a) ponder ponder (95% CI) (95% CI)(95% CI) Olanzapine 10 5 0.50 0.87 6.60 Olanzapine 10 33 (0.30 to 0.70)(0.73 to 0.94) (1.83 to 23.87) Olanzapine 10 5 0.67 0.64 3.60 Perphenazi5 9 (0.42 to 0.85) (0.39 to 0.84) (0.78 to 16.66) Olanzapine 10 5 0.590.69 3.14 Quetiapine 7 11 (0.36 to 0.78) (0.44 to 0.86) (0.75 to 13.16)Olanzapine 10 5 0.77 0.74 9.33 Rispiradon 3 14 (0.50 to 0.92) (0.51 to0.88) (1.80 to 48.38) Olanzapine 10 5 0.77 0.58 4.67 Ziprasidon 3 7(0.50 to 0.92) (0.32 to 0.81) (0.83 to 26.24) ^(a)A plus sign indicatesSULT4A1-1 positive and a negative sign indicates SULT4A1-1 negative^(b)Percent Positive Agreement = (true positive)/(true positive + falsenegative) = SULT4A1-1 positive olanzapine responders/all responders.^(c)Percent Negative Agreement = (true negative)/(true negative + falsepositive) = SULT4A1-1 negative nonresponders for comparator/allnonresponders ^(d)Diagnostic Odds Ratio = (True positive * truenegative)/(False positive * false negative)

Example 7 Additional Evidence For Correlation of the SULT4A Haplotypewith Baseline Psychopathology and Response to Atypical Antipsychotic inSchizophrenia and Related Disorders

Genotype and phenotype data for the CATIE trial were recently madeavailable to qualified researchers through The NIMH Center forCollaborative Genetic Studies on Mental Disorders. The inventorsevaluated data for 417 CATIE patients with schizophrenia self reportedas having exclusively European ancestry. This same patient populationwas described in a recent study by Sullivan and coworkers, whichconfirmed that there is no hidden stratification in the sample (Sullivanet al., 2008).

The CATIE clinical data set included baseline PANSS scores based onclinical assessments prior to initiation of the assigned therapy, butfollowing the washout period for any patients previously onantipsychotic medication. Follow up PANSS data for the CATIE trial werecollected at each visit as described in detail by others (Stroup et al.,2003). Briefly, the first visit was after one month of treatment, andsubsequent visits were at somewhat irregular intervals of approximatelythree months for up to a total 18 months or until discontinuation oftreatment, whichever came first.

As described above, the inventors evaluated the SULT4A1 gene. The CATIEgenotype data included a total of 11 SNPs located between the previouslyevaluated rs138110, in the promoter region, and the terminal exon of thegene (Brennan and Condra, 2005; Condra et al., 2007; Meltzer et al.,2008). From lowest to highest base pair position on the chromosome theCATIE SNPs were rs138067, rs138079, rs470089, rs2285161, rs2285162,rs2285164, rs2285167, rs470091, rs138099, rs138102, rs138110. Asdescribed below, these allowed unambiguous assignment of SULT4A1haplotype status.

The initial genetic analysis to determine the influence of SULT4A1haplotypes on quantitative PANSS values was performed using the PLINK1.03 whole genome analysis toolset developed by Purcell and coworkers(available at pngu.mgh.harvard.edu/purcell/plink/) (Purcell et al.,2007). This software assigns expectation-maximization (EM)algorithm—based haplotypes to each individual. Using these haplotypeassignments, PANSS Total scores were analyzed as quantitative traits inPLINK by linear regression.

The inventors used genotype data from the International HapMap projectto determine which alleles of rs138097 are associated with each of thesix common haplotypes identified by the EM algorithm in PLINK (availablevia world wide web at hapmap.org/cgi-perl/gbrowse/hapmap). Briefly, tenof the 11 CATIE SNPs (rs138067 being the exception) as well as rs138097were evaluated in 58 individuals of European ancestry (CEPH Collection)by the HapMap project. Precalculated linkage disequilibrium parametersshow that all ten of the other SNPs display D′ values of 1.0 withrs138097, each with robust statistical support (LOD scores≧2.7).Furthermore, the inventors evaluated genotypes for the 11 HapMap SNPsusing PLINK, and the EM algorithm identified the same six haplotypesthat the inventors observed in the CATIE sample, such that a givenallele of rs138097 is invariably associated with a specific haplotype(116 agreements out of 116 haplotype assignments).

For all subsequent analyses, the inventors focused on the singlehaplotype, designated SULT4A1-1. EM algorithm haplotypes were assignedto each patient using HelixTree software (Version 6.4.1; Golden Helix,Bozeman, Mont.), and each individual was scored as being positive ornegative for the presence of the haplotype. The inventors assignedSULT4A1-1 haplotype status to those individuals for which EM algorithmassignment could be made with error probabilities of <1%. This includeda total of 395 patients from the CATIE study. With the exception of fourof the 395 patients in the CATIE study, SULT4A1-1 haplotype status couldbe assigned with error probabilities of <1×10-5.

To determine the effect of SULT4A1-1 haplotype status on drug response,differences in percent change of PANSS scores from baseline in Phase Iof the CATIE trial were analyzed using a linear model with haplotype anddrug therapy status as predictors. Since follow-up on subjects was notdone at uniform time intervals, analysis was done using the lastobservation for each patient in treatment Phase I of the trial as themeasure of response (last observation carried forward, LOCF). Maineffect and interaction terms between the SULT4A1-1 haplotype and drugtherapy were included in the linear model. A pre-determined set ofcontrasts for differences in percent change PANSS by haplotype withineach drug therapy (three comparisons) and by drug therapy within eachhaplotype (six comparisons) were evaluated, with adjustment formultiple-comparisons using the step-up false-discovery rate (FDR)controlling procedure (Benjamini and Hochberg, 1995). A sub-analysisomitting those patients who were randomized to the same antipsychoticdrug therapy was also conducted.

The 11 SULT4A1 SNPs genotyped in the CATIE study make up a singlehaplotype block as determined by Haploview (FIG. 1; Barrett et al.,2005). E-M maximum likelihood phasing of the 11 SNPs from the CATIEstudy indicated that these markers define only six common haplotypes inCaucasians (Table 3 in Example 2). The haplotype designated SULT4A1-1occurs at a frequency of 11.6%.

The inventors wanted to test whether the SULT4A1-1 haplotype mightrelate to pharmacological response for the three atypical antipsychoticdrugs that were available for use throughout the CATIE study(olanzapine, quetiapine, and risperidone). As shown in Table 17,patients segregated by SULT4A1-1 haplotype status show differences inpercent reduction of PANSS according to the drug therapy received. Inparticular, SULT4A1-1 positive patients responded better to olanzapinethan do SULT4A1-1 negative patients, and SULT4A1-1 positive patientsalso responded better to olanzapine compared to the other two drugs. Forthe complete sample, the overall ANOVA F-test for differences inresponse rate by SULT4A1-1 haplotype/drug therapy was significant (Table17, top; p=0.035). Pairwise comparisons between SULT4A1-1 positive vsnegative patients on olanzapine, SULT4A1-1 positive patients takingolanzapine vs risperidone, and SULT4A1-1 positive patients takingolanzapine vs quetiapine all had significant unadjusted p-values, butdid not remain statistically significant after adjustment for the ninecomparisons (Table 18, top).

TABLE 17 Relationship of SULT4A1-1 Status to Atypical AntipsychoticResponse in CATIE ^(a) Haplotype status Olanzapine RisperidoneQuetiapine Complete Sample SULT4A1-1 + −20.5 (18.6) N = 17 −3.52 (18.6)N = 18 −4.52 (17.6) N = 20 SULT4A1-1 − −7.44 (22.1) N = 62 −4.28 (25.1)N = 67  0.84 (26.5) N = 63 Patients Randomized to a Different Medication^(b) SULT4A1-1 + −24.55 (17.2) N = 13 −1.86 (19.8) N = 15 −6.44 (19.0) N= 16 SULT4A1-1 −   −5.8 (21.7) N = 36  −4.3 (25.0) N = 55   0.4 (26.7) N= 56 ^(a) Percent change from baseline PANSS scores in Phase I of theCATIE study, based on the last observation carried forward (LOCF), means(standard deviation). ^(b) Data in the lower half of the table are forthe subset of patients who were assigned to a trial arm such that theyeither switched to a new medication after the washout period or were notpreviously stabilized on an antipsychotic drug.

TABLE 18 Pair-wise Comparisons for Change in Total PANSS in CATIE PhaseI Differ- 95% CI 95% CI Adjust- Comparison^(a) ence^(b) Lower Upper P edP Complete Sample Olanzapine, SULT4A1-1+ vs SULT4A1-1− −13.1 −25.6 −0.50.04 0.13 Risperidone, SULT4A1-1− vs SULT4A1-1+ −0.8 −13.2 11.7 0.900.90 Quetiapine, SULT4A1-1+ vs SULT4A1-1− −5.4 −17.4 6.7 0.37 0.57SULT4A1-1+, Olanzapine vs Risperidone −17.0 −32.8 −1.2 0.03 0.13SULT4A1-1+, Quetiapine vs Risperidone −1.0 −16.2 14.2 0.90 0.90SULT4A1-1+, Olanzapine vs Quetiapine −16.0 −31.4 −0.5 0.04 0.13SULT4A1-1−, Olanzapine vs Risperidone −3.2 −11.4 5.1 0.44 0.57SULT4A1-1−, Risperidone vs Quetiapine −5.1 −13.3 3.1 0.22 0.48SULT4A1-1−, Olanzapine vs Quetiapine −7.7 −25.3 9.9 0.38 0.57 PatientsRandomized to a Different Medication^(c) Olanzapine, SULT4A1-1+ vsSULT4A1-1− −18.8 −25.6 −0.5 0.015 0.07 Risperidone, SULT4A1-1− vsSULT4A1-1+ −2.5 −16.3 11.4 0.72 0.77 Quetiapine, SULT4A1-1+ vsSULT4A1-1− −6.8 −20.3 6.6 0.31 0.47 SULT4A1-1+, Olanzapine vsRisperidone −22.7 −40.6 −4.7 0.012 0.07 SULT4A1-1+, Quetiapine vsRisperidone −4.6 −21.6 12.4 0.59 0.77 SULT4A1-1+, Olanzapine vsQuetiapine −18.1 −35.8 −0.4 0.04 0.13 SULT4A1-1−, Olanzapine vsRisperidone −1.5 −11.7 8.7 0.77 0.77 SULT4A1-1−, Risperidone vsQuetiapine −4.7 −13.7 4.3 0.30 0.47 SULT4A1-1−, Olanzapine vs Quetiapine−11.9 −32.3 8.5 0.24 0.46 ^(a)Comparisons are listed such that the groupshowing superior performance is given first. ^(b)Difference in percentchange in PANSS score for the first group minus that for the secondgroup. The negative values (larger decrease in PANSS score) correspondto a greater response for the first group. ^(c)Data in the lower half ofthe table are for the subset of patients who were assigned to a trialarm such that they either switched to a new medication after the washoutperiod or were not previously stabilized on an antipsychotic drug.

The inventors examined patient sex, age and age of onset as possibleconfounders for drug response. Adjusting for patient age, age of onset,and gender in the linear model did not markedly alter the estimateddifferences in percent reduction of PANSS by drug therapy and SULT4A1-1haplotype (Table 19, top). In particular, the results for thedifferences with significant unadjusted p-values in Table 18 were notaltered.

TABLE 19 Pair-wise Comparisons for Change in Total PANSS in CATIE PhaseI Corrected for Age, Age of Onset and Sex 95% 95% Adj. Differ CI CI P PComparison ^(a) -ence ^(b) Lower Upper value value Olanzapine,SULT4A1-1 + vs SULT4A1-1 − −13.96 −25.62 −0.50 0.03 0.10 Risperidone,SULT4A1-1 − vs SULT4A1-1 + −2.48 −15.52 10.55 0.70 0.79 Quetiapine,SULT4A1-1 + vs SULT4A1-1 − −2.65 −15.20 9.91 0.67 0.79 SULT4A1-1 +,Olanzapine vs Risperidone −18.67 −35.31 −2.03 0.03 0.10 SULT4A1-1 +,Quetiapine vs Risperidone −0.54 −16.53 15.45 0.95 0.95 SULT4A1-1 +,Olanzapine vs Quetiapine −18.14 −34.21 −2.06 0.03 0.10 SULT4A1-1 −,Olanzapine vs Risperidone −2.23 −10.52 6.06 0.59 0.79 SULT4A1-1 −,Risperidone vs Quetiapine −4.60 −12.97 3.78 0.27 0.49 SULT4A1-1 −,Olanzapine vs Quetiapine −11.31 −29.43 6.82 0.21 0.48 PatientsRandomized to a Different Medication ^(c) 95% 95% Adj. Differ CI CI P PComparison -ence Lower Upper value value Olanzapine, SULT4A1-1 + vsSULT4A1-1 − −19.07 −25.62 −0.50 0.02 0.06 Risperidone, SULT4A1-1 − vsSULT4A1-1 + −5.14 −19.83 9.55 0.49 0.73 Quetiapine, SULT4A1-1 + vsSULT4A1-1 − −2.91 −16.84 11.03 0.68 0.80 SULT4A1-1 +, Olanzapine vsRisperidone −25.03 −44.22 −5.83 0.01 0.06 SULT4A1-1 +, Quetiapine vsRisperidone −3.33 −21.26 14.59 0.71 0.80 SULT4A1-1 +, Olanzapine vsQuetiapine −21.69 −40.20 −3.19 0.02 0.06 SULT4A1-1 −, Olanzapine vsRisperidone −0.82 −11.02 9.39 0.87 0.87 SULT4A1-1 −, Risperidone vsQuetiapine −4.71 −13.99 4.57 0.31 0.56 SULT4A1-1 −, Olanzapine vsQuetiapine −16.17 −37.32 4.98 0.13 0.29 ^(a) Comparisons are listed suchthat the group showing superior performance is given first. ^(b)Difference in percent change in PANSS score for the first group minusthat for the second group. The negative values (larger decrease in PANSSscore) correspond to a greater response for the first group. ^(c) Datain the lower half of the table are for the subset of patients who wereassigned to a trial arm such that they either switched to a newmedication after the washout period or were not previously stabilized onan antipsychotic drug.

To remove total length of time on drug treatment as potentialconfounding variable, the inventors additionally carried out analysis ofonly those patients who switched to a new medication or had notpreviously been on an antipsychotic medication prior to enrollment inthe CATIE study. Those who were randomized to the same medication may ormay not have reached a steady state in their response to that particulartreatment, in which case, the clinical response during the trial mightbe complicated by effects relating to the total length of time on thedrug and not a drug effect per se. Also, by looking only at the subgrouprandomized to a different medication, the inventors are able to assessdrug effects during the process of switching to a medication thatpatients are not currently taking.

When considering this subset of patients, the differences in percentreduction of PANSS by drug therapy and SULT4A1-1 haplotype are morepronounced (Table 17, bottom). The overall ANOVA F-test was againsignificant (p=0.037). Comparisons between SULT4A1-1 positive vsnegative patients on olanzapine, SULT4A1-1 positive patients takingolanzapine vs risperidone, and SULT4A1-1 positive patients takingolanzapine vs. quetiapine again all had significant unadjusted p-values,with the former two having marginal significance (p=0.07) afteradjustment for multiple comparisons (Table 18, bottom). Adjustment forpatient age, age of onset, and gender again did not impact the results(Table 19, bottom).

The inventors evaluated the feasibility of replicating these findingsusing the CATIE Phase II data, in which non-responders were subsequentlytreated with a different drug. Phase II cannot be considered an exactreplication of Phase I because the patient population in Phase II isexpected to be enriched for individuals who are resistant to treatmentby any antipsychotic drug. Indeed, improvement in PANSS scores was lesspronounced for all groups in Phase II (Table 20). Data were availablefor too few patients in Phase II for statistical analyses to be validfor the SULT4A1-1 positive group. However, for Phase II, SULT4A1-1positive patients did respond somewhat better than the SULT4A1-1negative patients to olanzapine. Also, this group displayed moreimprovement on olanzapine compared to either risperidone or quetiapine.

TABLE 20 CATIE Phase I non-responders last observation carry forward forPhase II (decrease PANSS ≧ 20%) SULT4A1-1 Drug Status RespondersNonresponders % Responders Olanzapine Positive 3 4 42.9 OlanzapineNegative 3 14 17.6 Risperidone Positive 0 1 0 Risperidone Negative 4 833.3 Quetiapine Positive 0 1 0 Quetiapine Negative 1 10 9.0

Example 8 Risk Management Involving SULT4A1-1 Test

The SULT4A1-1 test, as well as any test including a SULT4A1-1 haplotypedetermination, will be used in the risk-benefit analysis for prescribingatypical antipsychotics—olanzapine in particular. The highly variableefficacy of olanzapine and moderate to large side effect burden createan opportunity to greatly enhance patient care and usefulness ofolanzapine when combined with the SULT4A1-1 haplotype test.

The risk management program (an embodiment illustrated in FIG. 7) hasthe potential of becoming an FDA-mandated safety program for prescribingolanzapine vs. risperidone. By incorporating the SULT4A1-1 haplotypedetermination into an electronic data exchange that interfaces withphysicians, pharmacies labs and patients, this invention may be appliedto guide all of the four groups involved in selection of and dispensingof olanzapine utilizing information that will optimize potentialtherapeutic benefits (such as optimal efficacy and improvement ofsymptoms) and minimize potential risks (such as lack of drug effect andrisks associated with lack of drug effect like hospitalization andworsening of symptoms).

Example 9 Single SNP Determination for SULT4A1-1 Haplotype

Using the International HapMap Project resources (www.hapmap.org), theinventors downloaded pre-computed haplotypes for the SULT4A1 gene. Usingthe precomputed haplotypes, the inventors identified SNP allelesassociated with the SULT4A1-1 haplotype using the algorithm specifiedpreviously. The inventors searched for single SNPs that uniquelyidentified that haplotype and were able to identified rs763120 (the SNPis at position 31 at SEQ ID NO:15), C allele, as meeting that criterion.Subsequently the inventors used a sample of several hundred DNAs toconfirm that the C allele of rs763120 indeed marks the SULT4A1-1haplotype. Therefore, as one example, rs763120 can be used as a singleSNP test to tag the SULT4A1-1 haplotype.

Example 10 Segmentation by SULT4A1-1 Status Predicts DifferentialResponse to Risperidone

The CATIE clinical data set included Clinical Global Impression (CGI)Scale, an observer-provided assessment of the psychiatric health of thepatient (Stroup et al., 2003; Guy 1976). Patients are rated with the CGIScale from 1 to 7, with higher scores indicating greater severity ofillness. The CATIE study provided a response variable that measured thetime (in months) of successful treatment as measured by the CGI scale(“TMSUCC1” in the CATIE data).

Using SULT4A1-1 status based on evaluation of the CATIE genotype data(see Example 3), the inventors tested if SULT4A1-1 status can be used topredict the length of time for successful treatment with risperidone asmeasured by the CGI scale. Using this metric, as can be seen in Table21, SULT4A1-1 negative patients on risperidone have a higher averagenumber of months of successful treatment (6.88 months) than do SULT4A1-1positive patients on risperidone (1.76 months) with a p-value of 0.001.Furthermore, SULT4A1-1 positive patients show a shorter time ofsuccessful treatment when treated with risperidone compared to treatmentwith any of the other antipsychotic drugs.

TABLE 21 SULT4A1-1 Status Relates to Length of Successful Treatment withrisperidone (CGI Months) Unsegmented SULT4A1-1 positive SULT4A1-1negative Drug N^(a) Mean SD^(b) N^(a) Mean SD^(b) N^(a) Mean SD^(b)P-val Olanzapine 93 6.10 6.44 21  8.33^(d) 7.00 72 5.44 6.17 0.070Perphenazine 79 6.72 7.26 14 5.29 6.89 65 7.03 7.35 0.419 Quetiapine 974.65 6.14 24   5.96^(c) 6.75 73 4.22 5.91 0.230 Risperidone 98 5.79 6.6121 1.76 4.01 77 6.88 6.77 0.001 Ziprasidone 50 5.36 6.17 11  8.36^(d)7.49 39 4.51 5.56 0.067 ^(a)N corresponds to the number of samples.^(b)SD corresponds to standard deviation. ^(c)Statistically significantdifference in comparison with SULT4A1-1 positive risperidone withp-value < 0.05 ^(d)Statistically significant difference in comparisonwith SULT4A1-1 positive risperidone with p-value < 0.005

Example 11 SULT4A1-1 Positive Patients have an Elevated Risk ofDiscontinuation when Treated with Risperidone

Discontinuation of antipsychotic drug use is a major risk factor forantipsychotic drugs and can adversely impact the safety profile of thesemedications. Using the CATIE data, the inventors have shown thatSULTA1-1 haplotype status relates to the risk of discontinuing use ofrisperidone. For the analyses shown in Tables 22-24, SULT4A1-1 haplotypestatus was assigned as describe in Example 3, and standard statisticalsurvival analysis using Cox's proportional hazards model was used todetermine the relative risk (hazard) of discontinuing drug use. TheHazard Ratio (HR) measures the risk of an event (in this case, switchingor discontinuation from the drug) relative to patient exposure or status(in this case, SULT4A1-1 positive status). Hence, for example, a HR of 2means that SULT4A1-1 positive patients are twice as likely todiscontinue when compared to SULT4A1-1 negative patients, while a HR of0.5 means that SULT4A1-1 positive patients have 50% lower risk ofdiscontinuation compared to SULT4A1-1 negative patients.

When treated with risperidone, SULT4A1-1 positive patients have anelevated risk of discontinuation as measured by all-causediscontinuation. As can be seen in Table 22, SULT4A1-1 positive patientstreated with risperidone have an elevated risk of discontinuing drug usefor all-causes (HR=1.74) as compared to the SULT4A1-1 negative patientstreated with risperidone.

TABLE 22 Hazard of All-Cause Discontinuation in the CATIE StudyComparison HR 95% CI^(c) P-value Unsegmented risperidone/ 0.91^(a)(0.68, 1.23) 0.54 Unsegmented all other drugs SULT4A1-1 negativerisperidone/ 0.79^(a) (0.56, 1.12) 0.18 SULT4A1-1 negative all otherdrugs SULT4A1-1 positive risperidone/ 1.48^(a) (0.82, 2.6) 0.189SULT4A1-1 positive all other drugs SULT4A1-1 positive risperidone/SULT4A1-1 negative risperidone 1.74^(b) (0.98, 3.11) 0.06 ^(a)The HazardRatio (HR) of patient population on risperidone/those on otherantipsychotics. ^(b)The Hazard Ratio (HR) of SULT4A1-1 positive patientpopulation on risperidone/SULT4A1-1 negative patient population onrisperidone. ^(c)The data represents 95% confidence interval for themeasured Hazard Ratio (HR).

SULT4A1-1 positive patients treated with risperidone have an elevatedrisk of discontinuation due to lack of efficacy. As can be seen in Table23, SULT4A1-1 positive patients treated with risperidone have anelevated risk of discontinuing drug use due to lack of efficacy(HR=1.94) as compared to the SULT4A1-1 negative patients treated withrisperidone. Similarly, SULT4A1-1 positive patients treated withrisperidone have an elevated risk of discontinuation due to lack ofefficacy (HR=2.36) as compared to SULT4A1-1 positive patients treatedwith other antipsychotics

TABLE 23 Hazard of Discontinuation Due to Lack of Efficacy in the CATIEStudy Comparison HR 95% CI^(c) P-value Unsegmented risperidone/ 1.09^(a)(0.72, 1.65) 0.673 Unsegmented all other drugs SULT4A1-1 negativerisperidone/ 0.88^(a) (0.55, 1.43) 0.608 SULT4A1-1 negative all otherdrugs SULT4A1-1 positive risperidone/ 2.36^(a) (1.02, 5.57) 0.044SULT4A1-1 positive all other drugs SULT4A1-1 positive risperidone/1.94^(b) (0.89, 4.25) 0.095 SULT4A1-1 negative risperidone ^(a)TheHazard Ratio (HR) of patient population on risperidone/those on otherantipsychotics. ^(b)The Hazard Ratio (HR) of SULT4A1-1 positive patientpopulation on risperidone/SULT4A1-1 negative patient population onrisperidone. ^(c)The data represents 95% confidence interval for themeasured Hazard Ratio (HR).

SULT4A1-1 positive patients treated with risperidone have elevated riskof discontinuation due to treatment emergent side effects. As shown inTable 24, SULT4A1-1 positive patients treated with risperidone have anelevated risk of discontinuation due to treatment emergent side effects(HR=2.2) as compared to SULT4A1-1 negative patients treated withrisperidone. Further, SULT4A1-1 negative patients treated withrisperidone have lower risk of discontinuation due to treatment emergentside effects (HR=0.47) as compared to SULT4A1-1 negative patientstreated with other antipsychotics.

TABLE 24 Hazard of Discontinuation Due to Treatment Emergent SideEffects in the CATIE Study Comparison HR 95% CI^(c) P-value Unsegmentedrisperidone/ 0.52^(a) (0.28, 0.97) 0.0387 Unsegmented all other drugsSULT4A1-1 negative risperidone/ 0.47^(a) (0.22, 0.98) 0.044 SULT4A1-1negative all other drugs SULT4A1-1 positive risperidone/ 0.73^(a) (0.25,2.16) 0.573 SULT4A1-1 positive all other drugs SULT4A1-1 positiverisperidone/ 2.2^(b) (0.65, 7.21) 0.21 SULT4A1-1 negative risperidone^(a)The Hazard Ratio (HR) of patient population on risperidone/those onother antipsychotics. ^(b)The Hazard Ratio (HR) of SULT4A1-1 positivepatient population on risperidone/SULT4A1-1 negative patient populationon risperidone. ^(c)The data represents 95% confidence interval for themeasured Hazard Ratio (HR).

Example 12 SULT4A1-1 Negative Patients have an Elevated Risk ofDiscontinuation Due to Treatment-Emergent Adverse Events (TAES) WhenTreated with Olanzapine

The published results from the CATIE Study agree with previous findingsthat olanzapine has both a higher efficacy and a higher burden of weightgain and metabolic side-effect than the other antipsychotics (Liebermanet al. 2005). Specifically, the CATIE consortium found that olanzapinetreated patients stayed on the drug longer, had few discontinuations forlack of efficacy, and had a higher incidence of clinically significantweight gain compared to patients treated with other drugs.Interestingly, despite the higher incidence of weight gain, olanzapinewas not inferior to the other drugs, with exception of risperidone, intime to discontinuation for intolerability, suggesting that physiciansfound the weight gain manageable in light of the efficacy of the drug.

The CATIE data yielded safety information in the form oftreatment-emergent adverse events (TAEs) that can be used in conjunctionwith SULT4A1-1 status to impact the risk/benefit profile of usingolanzapine. Specifically, the inventors have shown that SULT4A1-1negative status predicts an elevated risk of discontinuing use due toTAE's for patients treated with olanzapine. All of the drugs studied inCATIE have significant side-effect burdens. Thus, an important outcomemeasure was time to discontinuation for TAE. While the various TAEs aretraditional safety measures that are reflected in the existing druglabels, segmentation by SULT4A1-1 haplotype status produces specialsubpopulations for which the rates and/or severity of the TAE arealtered and for which new label language may be appropriate (e.g., asseen for the drug metabolism enzymes). Accordingly, segmentation bySULT4A1-1 status can lead to an altered risk/benefit profile.

To demonstrate the impact of SULT4A1-1 haplotype status on time todiscontinuation for TAEs, SULT4A1-1 haplotype status was assigned asdescribe in Example 3, and standard statistical survival analysis usingCox's proportional hazards model was used to determine the relative risk(hazard) of discontinuing drug use was performed as described in Example11. As describe in Example 11, Hazard Ratio (HR) measures the risk of anevent (in this case, switching or discontinuation from the drug)relative to patient exposure or status (in this case, SULT4A1-1 status).

Table 25 shows how segmentation by SULT4A1-1 status impacts the riskthat olanzapine treated patients experience a TAE that forced adiscontinuation of therapy. For the unsegmented patient populationolanzapine has a higher risk of TAEs compared to the other drugs inCATIE (HR=1.6). However, segmentation by SULT4A1-1 status reveals thatthe enhanced risk is attributable to the SULT4A1-1 negative patients(HR=2.0) and not to SULT4A1-1 positive patients (HR<1.0). Therefore, bythis measure, olanzapine is less safe than other drugs for the SULT4A1-1negative patients, but not for SULT4A1-1 positive patients.

TABLE 25 Hazard of Discontinuation Due to TAEs for Olanzapine in theCATIE Study Comparison HR 95% CI^(C) P-value Unsegmented olanzapine/1.6^(a) (0.94, 2.7) 0.08 Unsegmented all other drugs SULT4A1-1 negativeolanzapine/ 2.0^(a) (1.1, 3.6) 0.03 SULT4A1-1 negative all other drugsSULT4A1-1 positive olanzapine/ 0.85^(a) (0.28, 2.6) 0.77 SULT4A1-1positive all other drugs SULT4A1-1 positive olanzapine/ 0.67^(b) (0.2,2.0) 0.48 SULT4A1-1 negative olanzapine ^(a)The Hazard Ratio (HR) ofpatient population on olanzapine/those on other antipsychotics includingrisperidone, quetiapine, ziprasidone, and perphenzazine ^(b)The HazardRatio (HR) of SULT4A1-1 (+) positive patient population onolanzapine/SULT4A1-1 (−) positive patient population on olanzapine.^(C)The data represent 95% confidence interval for the measured HazardRatio (HR).

Example 13 SULT4A1-1 Negative Patients have an Elevated Risk ofHospitalization for Psychosis when Treated with Quetiapine

A. Correlation of Haplotype Status with Hospitalization Due toExacerbation of Psychosis

Schizophrenia is a life-long, chronic illness. Often patients cyclebetween periods of well managed disease and periods of relapse orexacerbation of psychosis. One of the main goals of antipsychotictherapy is to prevent relapses of psychosis. Indeed, all of the atypicalantipsychotics used in the CATIE trial have specific label claims forthe maintenance of response. When the disease becomes uncontrolled,these relapses often lead to hospitalization. In CATIE, the averageduration of a hospital stay was 15.2 days incurring inpatients costs of˜$12,600 per stay, representing a significant burden on both the patientand the healthcare system. Additionally, during the relapse period,schizophrenics are at increased risk for harm to self and others. Whilerelapse and hospitalization are known risks associated with thetreatment failure for schizophrenia, identification of specialpopulations for which the rate or risk of these events is alteredconstitutes new safety information.

To assess if SULT4A1-1 status impacts the risk of hospitalization inCaucasians, the inventors assigned SULT4A1-1 status to each CATIEsubject and evaluated hospitalization events due to exacerbation ofpsychosis. For this analysis, the inventors assigned a dichotomous value(positive or negative) for hospitalization status to subjects in eachphase of the trial based on only the first hospitalization event for agiven patient in that phase. Patients participating in Phases 1, 2,and/or 3 were included in the totals for the appropriate drug. Table 26shows the results of that analysis.

TABLE 26 SULT4A1-1 Status and Rate of Hospitalization (HOSP) SULT4A1-1SULT4A1-1 Unsegmented negative Positive Drug N HOSP N HOSP N HOSPP-value¹ Olanzapine 162 23 124 22 38 1 0.016 (14.2%) (17.7%)  (2.6%)Perphenazine 81 10 67  9 14 1 1.0 (12.3%) (13.4%)  (7.1%) Quetiapine 15725 123 24 34 1 0.017 (15.9%) (19.5%)  (2.9%) Risperidone 159 20 123 1636 4 1.0 (12.6%)   (13%) (11.1%) Ziprasidone 110 13 82 11 28 2 0.51(11.8%) (13.4%)  (7.1%) Total 669 91 518 82 150 9 0.002 (13.6%) (15.8%)  (6%) ¹Fisher's exact test comparing SULT4A1-1 negative to SULT4A1-1positive subjects for each drug

As can be seen, for all drugs, SULT4A1-1 negative patients are morelikely than SULT4A1-1 positive patients to be hospitalized forpsychosis. This finding is statistically significant for the patientpopulation as a whole as well as for olanzapine and quetiapineindividually. SULT4A1-1 negative subjects treated with olanzapine hadsignificantly higher likelihood of hospitalization (17.7%) than didSULT4A1-1 positive subjects treated with olanzapine (2.6%). Similarly,SULT4A1-1 negative subjects treated with quetiapine had significantlyhigher likelihood of hospitalization (19.5%) than did SULT4A1-1 positivesubjects treated with quetiapine (2.9%).

Given the frequency and severity of this adverse event, subpopulationswith elevated rates of hospitalization constitute an unexpected safetysignal and that could provide valuable information for treatingphysicians. Indeed, as Table 26 shows, for the unsegmented populationoverall, hospitalization due to exacerbation of psychosis occurred at ahigh rate for a serious adverse event (13.6%).

B. Kaplan-Meier Survival Analysis

A Kaplan-Meier survival analysis was performed to determine whetherthere was a difference between the survival (hospitalization) rates forthe SULT4A1-1 negative and SULT4A1-1 positive patient populationstreated with each of the atypical antipsychotics. Survival plots modelthe fraction of the population that survived (i.e., no hospitalizationevent) as a function of time. There was a significant difference betweenthe survival rates for olanzapine (P=0.029) and quetiapine (P=0.016)patients, with SULT4A1-1 negative patients showing a decreasing survivalrate with time as compared to the SULT4A1-1 positive patients. Thissuggests that SULT4A1-1 negative patients on olanzapine or quetiapinehave a higher likelihood of hospitalization with time as compared to theSULT4A1-1 positive patients. While similar trends were observed forpatients treated with risperidone (P=0.299) or ziprasidone (P=0.326),the difference between the SULT4A1-1 negative and SULT4A1-1 positivepopulations was not statistically significant. These results are showngraphically in FIG. 8.

All of the methods disclosed and claimed herein can be made and executedwithout undue experimentation in light of the present disclosure. Whilethe compositions and methods of this invention have been described interms of preferred embodiments, it will be apparent to those of skill inthe art that variations may be applied to the methods and in the stepsor in the sequence of steps of the method described herein withoutdeparting from the concept, spirit and scope of the invention. Morespecifically, it will be apparent that certain agents which are bothchemically and physiologically related may be substituted for the agentsdescribed herein while the same or similar results would be achieved.All such similar substitutes and modifications apparent to those skilledin the art are deemed to be within the spirit, scope and concept of theinvention as defined by the appended claims.

REFERENCES

The following references, to the extent that they provide exemplaryprocedural or other details supplementary to those set forth herein, arespecifically incorporated herein by reference.

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1. A method for treating a human subject having or suspected of having apsychotic disorder comprising: a) selecting a subject that has beendetermined to have a SULTA1-1 haplotype, wherein the SULTA1-1 haplotypeis defined as a haplotype comprising a C allele at rs763120, acombination of an A allele at rs2285162 and a G allele at rs2285167, orthe combination of a T allele at rs2285166 and G allele at rs2285167,and treating the subject that has the SULT4A1-1 haplotype withquetiapine or olanzapine; or b) selecting a subject that has beendetermined not to have the SULT4A1-1 haplotype and treating the subjectthat does not have the SULT4A1-1 haplotype with an anti-psychotictreatment other than quetiapine or olanzapine.
 2. The method of claim 1,wherein the subject comprises the SUTL4A1-1 haplotype and the subject istreated with quetiapine.
 3. The method of claim 1, wherein the subjectcomprises the SUTL4A1-1 haplotype and the subject is treated witholanzapine.
 4. The method of claim 1, wherein the subject does notcomprise the SULT4A1-1 haplotype and the subject is treated with ananti-psychotic treatment other than quetiapine or olanzapine.
 5. Themethod of claim 4, wherein the anti-psychotic treatment other thanquetiapine or olanzapine is risperidone.
 6. The method of claim 4,wherein the anti-psychotic treatment other than quetiapine or olanzapineis perphenazine.
 7. The method of claim 4, wherein the anti-psychotictreatment other than quetiapine or olanzapine is ziprasidone.
 8. Themethod of claim 1, wherein the psychotic disorder is schizophrenia.